Selecting genotypes for a specific chromosome belonging to a specific patient from a multi patient VCF file
I have a VCF file called HG002-HG003-HG004.jointVC.filter.vcf that consists of data from three patients. I am interested in isolating the genotypes for chr19 from patient HG002 only. Is there a way to do this using vcftools or alternative package? And can anyone recommend a manual or an example on how to accomplish this?
2 answers
Hi,
You could try bcftools. something like this:
bgzip -c HG002-HG003-HG004.jointVC.filter.vcf > HG002-HG003-HG004.jointVC.filter.vcf.gz
tabix -p vcf HG002-HG003-HG004.jointVC.filter.vcf.gz
bcftools view -s HG002 -r chr19 HG002-HG003-HG004.jointVC.filter.vcf.gz >HG002.chr19.vcf
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Hi,
You should compress and index your vcf file before
bgzip -c file.vcf > file.vcf.gz
tabix -p vcf file.vcf.gz
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grep "HG002" HG002-HG003-HG004.jointVC.filter_Annotated.vcf #finds patient ID, for use with [--indv]
vcftools --vcf HG002-HG003-HG004.jointVC.filter_Annotated.vcf --chr 19 --indv Sample_Diag-excap51-HG002-EEogPU --out HG002-chr19.vcf --recode
Found that is this works to generate a file consisting of only chr19 coordinates from patient HG002
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