Aoyue's note

2020-08-18

[toc]

一条染色体的测试，画MAF图

程序如下：

java -Xmx100g -jar TIGER_v1.0.1.jar -a HapScanner -p ./parameters_036_abd_hapScanner.txt > log_036_abd_hapScanner2.txt 2>&1 &
  • chr036 一共合并 call 出 19051 个 Indel, 在 六倍体中 maf 等于0的有 7885 个,小于0.01且不等于0的有 5003 个， 剩余11166 个。
  • maf 小于 0.01 的有 12888/19051 占比：0.6764
    结论：14213456个indel中，预计保留 14213456*0.3236 = 4599474

路径大全

HapScanner VCF file 文件路径

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cd /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/d
cd /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/d/out/VCF

cd /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd
cd /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF

cd /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/ab
cd /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/ab/out/VCF

bcftools 合并后的VCF文件路径

cd /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner

过滤MAF MISS OCCURRENCE 后的VCF文件路

cd /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel

log

cd /data4/home/aoyue/vmap2/analysis/023_hapScanner_basedPopDepth/log/004

Pipeline

Step1: bgzip and build vcf index

abd

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bgzip -@ 4 chr001.vcf && tabix -p vcf chr001.vcf.gz &
bgzip -@ 4 chr002.vcf && tabix -p vcf chr002.vcf.gz &
bgzip -@ 4 chr003.vcf && tabix -p vcf chr003.vcf.gz &
bgzip -@ 4 chr004.vcf && tabix -p vcf chr004.vcf.gz &
bgzip -@ 4 chr005.vcf && tabix -p vcf chr005.vcf.gz &
bgzip -@ 4 chr006.vcf && tabix -p vcf chr006.vcf.gz &
bgzip -@ 4 chr007.vcf && tabix -p vcf chr007.vcf.gz &
bgzip -@ 4 chr008.vcf && tabix -p vcf chr008.vcf.gz &
bgzip -@ 4 chr009.vcf && tabix -p vcf chr009.vcf.gz &
bgzip -@ 4 chr010.vcf && tabix -p vcf chr010.vcf.gz &
bgzip -@ 4 chr011.vcf && tabix -p vcf chr011.vcf.gz &
bgzip -@ 4 chr012.vcf && tabix -p vcf chr012.vcf.gz &
bgzip -@ 4 chr013.vcf && tabix -p vcf chr013.vcf.gz &
bgzip -@ 4 chr014.vcf && tabix -p vcf chr014.vcf.gz &
bgzip -@ 4 chr015.vcf && tabix -p vcf chr015.vcf.gz &
bgzip -@ 4 chr016.vcf && tabix -p vcf chr016.vcf.gz &
bgzip -@ 4 chr017.vcf && tabix -p vcf chr017.vcf.gz &
bgzip -@ 4 chr018.vcf && tabix -p vcf chr018.vcf.gz &
bgzip -@ 4 chr019.vcf && tabix -p vcf chr019.vcf.gz &
bgzip -@ 4 chr020.vcf && tabix -p vcf chr020.vcf.gz &
bgzip -@ 4 chr021.vcf && tabix -p vcf chr021.vcf.gz &
bgzip -@ 4 chr022.vcf && tabix -p vcf chr022.vcf.gz &
bgzip -@ 4 chr023.vcf && tabix -p vcf chr023.vcf.gz &
bgzip -@ 4 chr024.vcf && tabix -p vcf chr024.vcf.gz &
bgzip -@ 4 chr025.vcf && tabix -p vcf chr025.vcf.gz &
bgzip -@ 4 chr026.vcf && tabix -p vcf chr026.vcf.gz &
bgzip -@ 4 chr027.vcf && tabix -p vcf chr027.vcf.gz &
bgzip -@ 4 chr028.vcf && tabix -p vcf chr028.vcf.gz &
bgzip -@ 4 chr029.vcf && tabix -p vcf chr029.vcf.gz &
bgzip -@ 4 chr030.vcf && tabix -p vcf chr030.vcf.gz &
bgzip -@ 4 chr031.vcf && tabix -p vcf chr031.vcf.gz &
bgzip -@ 4 chr032.vcf && tabix -p vcf chr032.vcf.gz &
bgzip -@ 4 chr033.vcf && tabix -p vcf chr033.vcf.gz &
bgzip -@ 4 chr034.vcf && tabix -p vcf chr034.vcf.gz &
bgzip -@ 4 chr035.vcf && tabix -p vcf chr035.vcf.gz &
bgzip -@ 4 chr036.vcf && tabix -p vcf chr036.vcf.gz &
bgzip -@ 4 chr037.vcf && tabix -p vcf chr037.vcf.gz &
bgzip -@ 4 chr038.vcf && tabix -p vcf chr038.vcf.gz &
bgzip -@ 4 chr039.vcf && tabix -p vcf chr039.vcf.gz &
bgzip -@ 4 chr040.vcf && tabix -p vcf chr040.vcf.gz &
bgzip -@ 4 chr041.vcf && tabix -p vcf chr041.vcf.gz &
bgzip -@ 4 chr042.vcf && tabix -p vcf chr042.vcf.gz &
cd /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF

ab

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bgzip -@ 4 chr001.vcf && tabix -p vcf chr001.vcf.gz &
bgzip -@ 4 chr002.vcf && tabix -p vcf chr002.vcf.gz &
bgzip -@ 4 chr003.vcf && tabix -p vcf chr003.vcf.gz &
bgzip -@ 4 chr004.vcf && tabix -p vcf chr004.vcf.gz &
bgzip -@ 4 chr007.vcf && tabix -p vcf chr007.vcf.gz &
bgzip -@ 4 chr008.vcf && tabix -p vcf chr008.vcf.gz &
bgzip -@ 4 chr009.vcf && tabix -p vcf chr009.vcf.gz &
bgzip -@ 4 chr010.vcf && tabix -p vcf chr010.vcf.gz &
bgzip -@ 4 chr013.vcf && tabix -p vcf chr013.vcf.gz &
bgzip -@ 4 chr014.vcf && tabix -p vcf chr014.vcf.gz &
bgzip -@ 4 chr015.vcf && tabix -p vcf chr015.vcf.gz &
bgzip -@ 4 chr016.vcf && tabix -p vcf chr016.vcf.gz &
bgzip -@ 4 chr019.vcf && tabix -p vcf chr019.vcf.gz &
bgzip -@ 4 chr020.vcf && tabix -p vcf chr020.vcf.gz &
bgzip -@ 4 chr021.vcf && tabix -p vcf chr021.vcf.gz &
bgzip -@ 4 chr022.vcf && tabix -p vcf chr022.vcf.gz &
bgzip -@ 4 chr025.vcf && tabix -p vcf chr025.vcf.gz &
bgzip -@ 4 chr026.vcf && tabix -p vcf chr026.vcf.gz &
bgzip -@ 4 chr027.vcf && tabix -p vcf chr027.vcf.gz &
bgzip -@ 4 chr028.vcf && tabix -p vcf chr028.vcf.gz &
bgzip -@ 4 chr031.vcf && tabix -p vcf chr031.vcf.gz &
bgzip -@ 4 chr032.vcf && tabix -p vcf chr032.vcf.gz &
bgzip -@ 4 chr033.vcf && tabix -p vcf chr033.vcf.gz &
bgzip -@ 4 chr034.vcf && tabix -p vcf chr034.vcf.gz &
bgzip -@ 4 chr037.vcf && tabix -p vcf chr037.vcf.gz &
bgzip -@ 4 chr038.vcf && tabix -p vcf chr038.vcf.gz &
bgzip -@ 4 chr039.vcf && tabix -p vcf chr039.vcf.gz &
bgzip -@ 4 chr040.vcf && tabix -p vcf chr040.vcf.gz &
cd /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/ab/out/VCF

Step2: bcftools merge

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/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr001.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/ab/out/VCF/chr001.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr001.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr002.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/ab/out/VCF/chr002.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr002.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr003.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/ab/out/VCF/chr003.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr003.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr004.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/ab/out/VCF/chr004.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr004.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr005.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/d/out/VCF/chr005.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr005.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr006.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/d/out/VCF/chr006.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr006.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr007.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/ab/out/VCF/chr007.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr007.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr008.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/ab/out/VCF/chr008.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr008.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr009.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/ab/out/VCF/chr009.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr009.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr010.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/ab/out/VCF/chr010.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr010.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr011.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/d/out/VCF/chr011.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr011.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr012.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/d/out/VCF/chr012.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr012.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr013.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/ab/out/VCF/chr013.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr013.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr014.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/ab/out/VCF/chr014.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr014.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr015.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/ab/out/VCF/chr015.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr015.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr016.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/ab/out/VCF/chr016.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr016.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr017.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/d/out/VCF/chr017.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr017.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr018.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/d/out/VCF/chr018.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr018.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr019.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/ab/out/VCF/chr019.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr019.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr020.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/ab/out/VCF/chr020.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr020.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr021.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/ab/out/VCF/chr021.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr021.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr022.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/ab/out/VCF/chr022.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr022.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr023.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/d/out/VCF/chr023.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr023.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr024.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/d/out/VCF/chr024.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr024.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr025.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/ab/out/VCF/chr025.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr025.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr026.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/ab/out/VCF/chr026.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr026.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr027.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/ab/out/VCF/chr027.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr027.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr028.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/ab/out/VCF/chr028.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr028.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr029.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/d/out/VCF/chr029.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr029.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr030.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/d/out/VCF/chr030.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr030.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr031.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/ab/out/VCF/chr031.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr031.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr032.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/ab/out/VCF/chr032.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr032.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr033.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/ab/out/VCF/chr033.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr033.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr034.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/ab/out/VCF/chr034.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr034.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr035.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/d/out/VCF/chr035.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr035.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr036.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/d/out/VCF/chr036.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr036.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr037.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/ab/out/VCF/chr037.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr037.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr038.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/ab/out/VCF/chr038.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr038.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr039.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/ab/out/VCF/chr039.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr039.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr040.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/ab/out/VCF/chr040.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr040.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr041.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/d/out/VCF/chr041.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr041.vcf &
/data1/programs/bcftools-1.8/bcftools merge -m all --force-samples -f PASS,. --threads 8 /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/abd/out/VCF/chr042.vcf.gz /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/d/out/VCF/chr042.vcf.gz -o /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr042.vcf &
cd /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner

Step3: filter by maf>=0.01, Occurrence>=2, Miss<=0.2

结果文件

cd /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel

日志文件目录

cd /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence

运行程序

Note: -Xms -Xmx 根据服务器大小进行设置，在数据量非常小的情况下，也可以不设置。

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java -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr001.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr001.vcf 2 >&1 &
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr002.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr002.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr003.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr003.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr004.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr004.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr005.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr005.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr006.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr006.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr007.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr007.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr008.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr008.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr009.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr009.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr010.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr010.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr011.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr011.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr012.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr012.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr013.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr013.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr014.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr014.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr015.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr015.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr016.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr016.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr017.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr017.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr018.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr018.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr019.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr019.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr020.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr020.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr021.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr021.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr022.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr022.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr023.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr023.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr024.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr024.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr025.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr025.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr026.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr026.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr027.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr027.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr028.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr028.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr029.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr029.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr030.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr030.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr031.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr031.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr032.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr032.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr033.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr033.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr034.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr034.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr035.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr035.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr036.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr036.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr037.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr037.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr038.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr038.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr039.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr039.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr040.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr040.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr041.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr041.vcf
java -Xms200g -Xmx200g -jar 044_filterMafOccurrenceMiss.jar /data4/home/aoyue/vmap2/genotype/mergedVCF/106_MergedIndel_fromHapScanner/chr042.vcf /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence/log_chr042.vcf

脚本运行
nohup sh sh_java.sh > log_java_20200819.txt 2>&1 &
nohup sh sh_java2.sh > log_filtermaf_Indel.txt 2>&1 &

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cd /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel
cd /data4/home/aoyue/vmap2/analysis/029_hapScanner_onlyIndel/log_filterMafMissOccurrence
ls|xargs cat|grep complete

Step4: 修改名字

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mv chr001_occu2_maf0.01_miss0.2.vcf chr001_vmap2.0.vcf
mv chr002_occu2_maf0.01_miss0.2.vcf chr002_vmap2.0.vcf
mv chr003_occu2_maf0.01_miss0.2.vcf chr003_vmap2.0.vcf
mv chr004_occu2_maf0.01_miss0.2.vcf chr004_vmap2.0.vcf
mv chr005_occu2_maf0.01_miss0.2.vcf chr005_vmap2.0.vcf
mv chr006_occu2_maf0.01_miss0.2.vcf chr006_vmap2.0.vcf
mv chr007_occu2_maf0.01_miss0.2.vcf chr007_vmap2.0.vcf
mv chr008_occu2_maf0.01_miss0.2.vcf chr008_vmap2.0.vcf
mv chr009_occu2_maf0.01_miss0.2.vcf chr009_vmap2.0.vcf
mv chr010_occu2_maf0.01_miss0.2.vcf chr010_vmap2.0.vcf
mv chr011_occu2_maf0.01_miss0.2.vcf chr011_vmap2.0.vcf
mv chr012_occu2_maf0.01_miss0.2.vcf chr012_vmap2.0.vcf
mv chr013_occu2_maf0.01_miss0.2.vcf chr013_vmap2.0.vcf
mv chr014_occu2_maf0.01_miss0.2.vcf chr014_vmap2.0.vcf
mv chr015_occu2_maf0.01_miss0.2.vcf chr015_vmap2.0.vcf
mv chr016_occu2_maf0.01_miss0.2.vcf chr016_vmap2.0.vcf
mv chr017_occu2_maf0.01_miss0.2.vcf chr017_vmap2.0.vcf
mv chr018_occu2_maf0.01_miss0.2.vcf chr018_vmap2.0.vcf
mv chr019_occu2_maf0.01_miss0.2.vcf chr019_vmap2.0.vcf
mv chr020_occu2_maf0.01_miss0.2.vcf chr020_vmap2.0.vcf
mv chr021_occu2_maf0.01_miss0.2.vcf chr021_vmap2.0.vcf
mv chr022_occu2_maf0.01_miss0.2.vcf chr022_vmap2.0.vcf
mv chr023_occu2_maf0.01_miss0.2.vcf chr023_vmap2.0.vcf
mv chr024_occu2_maf0.01_miss0.2.vcf chr024_vmap2.0.vcf
mv chr025_occu2_maf0.01_miss0.2.vcf chr025_vmap2.0.vcf
mv chr026_occu2_maf0.01_miss0.2.vcf chr026_vmap2.0.vcf
mv chr027_occu2_maf0.01_miss0.2.vcf chr027_vmap2.0.vcf
mv chr028_occu2_maf0.01_miss0.2.vcf chr028_vmap2.0.vcf
mv chr029_occu2_maf0.01_miss0.2.vcf chr029_vmap2.0.vcf
mv chr030_occu2_maf0.01_miss0.2.vcf chr030_vmap2.0.vcf
mv chr031_occu2_maf0.01_miss0.2.vcf chr031_vmap2.0.vcf
mv chr032_occu2_maf0.01_miss0.2.vcf chr032_vmap2.0.vcf
mv chr033_occu2_maf0.01_miss0.2.vcf chr033_vmap2.0.vcf
mv chr034_occu2_maf0.01_miss0.2.vcf chr034_vmap2.0.vcf
mv chr035_occu2_maf0.01_miss0.2.vcf chr035_vmap2.0.vcf
mv chr036_occu2_maf0.01_miss0.2.vcf chr036_vmap2.0.vcf
mv chr037_occu2_maf0.01_miss0.2.vcf chr037_vmap2.0.vcf
mv chr038_occu2_maf0.01_miss0.2.vcf chr038_vmap2.0.vcf
mv chr039_occu2_maf0.01_miss0.2.vcf chr039_vmap2.0.vcf
mv chr040_occu2_maf0.01_miss0.2.vcf chr040_vmap2.0.vcf
mv chr041_occu2_maf0.01_miss0.2.vcf chr041_vmap2.0.vcf
mv chr042_occu2_maf0.01_miss0.2.vcf chr042_vmap2.0.vcf

Step5: calculate Indel and make table

在HPC上计数

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java -jar 043_countSitesinFastCallformat.jar  /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel > log_043_countSitesinFastCallformat_fixVMap2.0Indels_20200818.txt 2>&1 &
cat /data4/home/aoyue/vmap2/aaPlantGenetics/log_043_countSitesinFastCallformat_fixVMap2.0Indels_20200818.txt

转化表格

①将数据放入特定目录下，运行程序

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CountSites.mergeChr1and2txt_int("/Users/Aoyue/project/wheatVMapII/003_dataAnalysis/005_vcf/029_countSiteSummary/002_vmap2.0/log_043_countSitesinFastCallformat_fixVMap2.0Indels_20200818.txt","/Users/Aoyue/project/wheatVMapII/003_dataAnalysis/005_vcf/029_countSiteSummary/002_vmap2.0/CountVariants_fixVMap2.0_Indel_20200818.txt");

Step6: 压缩并建立索引

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cd /data4/home/aoyue/vmap2/genotype/mergedVCF/107_VMap2.0_Indel
bgzip chr001_vmap2.0.vcf && tabix -p vcf chr001_vmap2.0.vcf.gz &
bgzip chr002_vmap2.0.vcf && tabix -p vcf chr002_vmap2.0.vcf.gz &
bgzip chr003_vmap2.0.vcf && tabix -p vcf chr003_vmap2.0.vcf.gz &
bgzip chr004_vmap2.0.vcf && tabix -p vcf chr004_vmap2.0.vcf.gz &
bgzip chr005_vmap2.0.vcf && tabix -p vcf chr005_vmap2.0.vcf.gz &
bgzip chr006_vmap2.0.vcf && tabix -p vcf chr006_vmap2.0.vcf.gz &
bgzip chr007_vmap2.0.vcf && tabix -p vcf chr007_vmap2.0.vcf.gz &
bgzip chr008_vmap2.0.vcf && tabix -p vcf chr008_vmap2.0.vcf.gz &
bgzip chr009_vmap2.0.vcf && tabix -p vcf chr009_vmap2.0.vcf.gz &
bgzip chr010_vmap2.0.vcf && tabix -p vcf chr010_vmap2.0.vcf.gz &
bgzip chr011_vmap2.0.vcf && tabix -p vcf chr011_vmap2.0.vcf.gz &
bgzip chr012_vmap2.0.vcf && tabix -p vcf chr012_vmap2.0.vcf.gz &
bgzip chr013_vmap2.0.vcf && tabix -p vcf chr013_vmap2.0.vcf.gz &
bgzip chr014_vmap2.0.vcf && tabix -p vcf chr014_vmap2.0.vcf.gz &
bgzip chr015_vmap2.0.vcf && tabix -p vcf chr015_vmap2.0.vcf.gz &
bgzip chr016_vmap2.0.vcf && tabix -p vcf chr016_vmap2.0.vcf.gz &
bgzip chr017_vmap2.0.vcf && tabix -p vcf chr017_vmap2.0.vcf.gz &
bgzip chr018_vmap2.0.vcf && tabix -p vcf chr018_vmap2.0.vcf.gz &
bgzip chr019_vmap2.0.vcf && tabix -p vcf chr019_vmap2.0.vcf.gz &
bgzip chr020_vmap2.0.vcf && tabix -p vcf chr020_vmap2.0.vcf.gz &
bgzip chr021_vmap2.0.vcf && tabix -p vcf chr021_vmap2.0.vcf.gz &
bgzip chr022_vmap2.0.vcf && tabix -p vcf chr022_vmap2.0.vcf.gz &
bgzip chr023_vmap2.0.vcf && tabix -p vcf chr023_vmap2.0.vcf.gz &
bgzip chr024_vmap2.0.vcf && tabix -p vcf chr024_vmap2.0.vcf.gz &
bgzip chr025_vmap2.0.vcf && tabix -p vcf chr025_vmap2.0.vcf.gz &
bgzip chr026_vmap2.0.vcf && tabix -p vcf chr026_vmap2.0.vcf.gz &
bgzip chr027_vmap2.0.vcf && tabix -p vcf chr027_vmap2.0.vcf.gz &
bgzip chr028_vmap2.0.vcf && tabix -p vcf chr028_vmap2.0.vcf.gz &
bgzip chr029_vmap2.0.vcf && tabix -p vcf chr029_vmap2.0.vcf.gz &
bgzip chr030_vmap2.0.vcf && tabix -p vcf chr030_vmap2.0.vcf.gz &
bgzip chr031_vmap2.0.vcf && tabix -p vcf chr031_vmap2.0.vcf.gz &
bgzip chr032_vmap2.0.vcf && tabix -p vcf chr032_vmap2.0.vcf.gz &
bgzip chr033_vmap2.0.vcf && tabix -p vcf chr033_vmap2.0.vcf.gz &
bgzip chr034_vmap2.0.vcf && tabix -p vcf chr034_vmap2.0.vcf.gz &
bgzip chr035_vmap2.0.vcf && tabix -p vcf chr035_vmap2.0.vcf.gz &
bgzip chr036_vmap2.0.vcf && tabix -p vcf chr036_vmap2.0.vcf.gz &
bgzip chr037_vmap2.0.vcf && tabix -p vcf chr037_vmap2.0.vcf.gz &
bgzip chr038_vmap2.0.vcf && tabix -p vcf chr038_vmap2.0.vcf.gz &
bgzip chr039_vmap2.0.vcf && tabix -p vcf chr039_vmap2.0.vcf.gz &
bgzip chr040_vmap2.0.vcf && tabix -p vcf chr040_vmap2.0.vcf.gz &
bgzip chr041_vmap2.0.vcf && tabix -p vcf chr041_vmap2.0.vcf.gz &
bgzip chr042_vmap2.0.vcf && tabix -p vcf chr042_vmap2.0.vcf.gz &

Step7: 和VMap2.0进行合并, 压缩并建立索引

  • 将2020-05 VMap2.0 (i.e. hapscanner并过滤 MAF>=0.01 Miss<=0.2 Occurrence >=2) 中的 SNP 和Indel 结果只保留SNP(include biallelic and tri-allelic SNP)
  • 将2020-08 新做出来Indel (revised hapscanner output –> 并过滤 MAF>=0.01 Miss<=0.2 Occurrence >=2) 和上文SNP排序并合并
  • 见 java finalizeVMapII 方法

Step8: 最终核查所有染色体位点数是否一致,很重要的一步。

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java -jar 043_countSitesinFastCallformat.jar  /data4/home/aoyue/vmap2/genotype/mergedVCF/108_VMap2.0_final > log_043_countSitesinFastCallformat_fixVMap2.0_20200823.txt 2>&1 &
cat /data4/home/aoyue/vmap2/aaPlantGenetics/log_043_countSitesinFastCallformat_fixVMap2.0_20200823.txt

Step9: 建立md5，确定最终版,并拷贝至移动硬盘保存

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ls *.gz|xargs -I file echo "md5sum file > file.md5" > md5.sh
cp -Rf /data4/home/aoyue/vmap2/genotype/mergedVCF/108_VMap2.0_final/* /mnt/usb/WheatVariationMapII/VMapII/VMap2.0 &