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Old 11-04-2012, 07:58 AM   #2
Gig77
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Location: Canada

Join Date: Jun 2012
Posts: 17
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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
Options:
-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.
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