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Old 11-03-2012, 02:33 PM   #1
Location: Germany

Join Date: Aug 2012
Posts: 25
Default Splitting multiple sample vcf file

A question appears when working with vcf file produced by UnifiedGenotyper on multiple samples. It is of course better to work with single sample vcf file so I was trying to split the multiple sampel vcf file. I used vcf-subset of vcftools but the problem is that the splitted single sample vcf file still has homozygous reference calls. Does anyone has a easy solution to this problem?
yl01 is offline   Reply With Quote
Old 11-04-2012, 06:58 AM   #2
Location: Canada

Join Date: Jun 2012
Posts: 17

Have you tried the -e parameter? I suppose -a should also be used to get rid of alternate alleles not found in the subset.

Here is the usage of vcf-subset:

Usage: vcf-subset [OPTIONS] in.vcf.gz > out.vcf
-a, --trim-alt-alleles Remove alternate alleles if not found in the subset
-c, --columns <string> File or comma-separated list of columns to keep in the vcf file. If file, one column per row
-e, --exclude-ref Exclude rows not containing variants.
-f, --force Proceed anyway even if VCF does not contain some of the samples.
-p, --private Print only rows where only the subset columns carry an alternate allele.
-r, --replace-with-ref Replace the excluded types with reference allele instead of dot.
-t, --type <list> Comma-separated list of variant types to include: SNPs,indels.
-u, --keep-uncalled Do not exclude rows without calls.
-h, -?, --help This help message.
Gig77 is offline   Reply With Quote
Old 11-05-2012, 02:32 AM   #3
Location: Germany

Join Date: Aug 2012
Posts: 25

Thanks Gig77 for the answer! I tested with -e and it gave what I wanted.
yl01 is offline   Reply With Quote

unifiedgenotyper, vcf

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