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Old 04-19-2016, 09:48 PM   #1
watermelon1037
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Location: bay area

Join Date: Apr 2016
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Default A problem of using Samtools to make VCF file

Hi!

I used the samtools commands and 1000 genome data(phase 3, low-coverage sequenced data) to generate the VCF file for both snp and indel, and below are the two command lines to get the vcf file for 5 people. The final "5genomes.var.flt.vcf" file has around 163432 snp and indel sites. However, when I used the same way to generate the vcf file for 100 people, the final vcf file includes only 1465 snp and indel, which is too few. I checked the last locus for both files, it looks like both of them processed the whole chromosome 20.

Do you have any idea what's wrong with it?

Thanks a lot. I look forward to your reply.

————— Here are the commands I used to generate VCF file——————

../samtools-0.1.19/samtools mpileup -uf ../human_g1k_v37.fasta HG00096.chrom20.ILLUMINA.bwa.GBR.low_coverage.20120522.bam HG 00268.chrom20.ILLUMINA.bwa.FIN.low_coverage.20130415.bam HG00419.chrom20.ILLUMINA.bwa.CHS.low_coverage.20130415.bam HG00759. chrom20.ILLUMINA.bwa.CDX.low_coverage.20130415.bam HG01112.chrom2 0.ILLUMINA.bwa.CLM.low_coverage.20120522.bam | ../samtools-0.1.19/bcftools/bcftools view -bvc - > 5genomes.var.raw.bcf


../samtools-0.1.19/bcftools/bcftools view 5genomes.var.raw.bcf | ../samtools-0.1.19/bcftools/vcfutils.pl varFilter -D100 > 5genomes.var.flt.vcf
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