Question: A problem of using Samtools to make VCF file
gravatar for watermelon1037
4.0 years ago by
watermelon10370 wrote:

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?

Furthermore, in some others' VCF file generated by Samtools, for the ALT field, it includes the 'X' in many cases, but in my VCF files, the non-ref base 'X' never show up.I used the samtools-0.1.19 version. Would someone be able to clarify?

Thanks a lot. I look forward to your reply.

————— Here are the commands I used to generate VCF files: ————————————————————

../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/ varFilter -D100 > 5genomes.var.flt.vcf
snp samtools vcf indel • 1.4k views
ADD COMMENTlink modified 4.0 years ago by maiziex0 • written 4.0 years ago by watermelon10370

Since you're using an old version of samtools you'll never see 'X' as a non-ref base.

ADD REPLYlink written 4.0 years ago by Devon Ryan94k
gravatar for maiziex
4.0 years ago by
maiziex0 wrote:

should this use reference file for chromosome 20?

ADD COMMENTlink written 4.0 years ago by maiziex0
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