Selecting genotypes for a specific chromosome belonging to a specific patient from a multi patient VCF file

Question

[dk0319]

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?

Answer 1

[desouzareis.r]

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

[dk0319]

I tried this command and got this error.

Failed to open HG002-HG003-HG004.jointVC.filter_Annotated.vcf: not compressed with bgzip

Any idea how to correct this?

[desouzareis.r]

Hi,

You should compress and index your vcf file before

bgzip -c file.vcf > file.vcf.gz
tabix -p vcf file.vcf.gz

Answer 2

[dk0319]

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

[GenoMax]

Use programs meant for handling VCF files whenever possible. Utilities like grep may miss subtle things.