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  • 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?

  • #2
    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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    • #3
      Thanks Gig77 for the answer! I tested with -e and it gave what I wanted.

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      • #4
        If you want to Split Large sized VCF Files of Vcards into Smaller ones, then you can try our most efficient VCF Splitter Tool. The utility can easily divide the VCF files with all the contacts and other files without any data loss. If you want to Split Large sized VCF Files of vCard into Smaller ones, then you can try our most efficient VCF Splitter Tool.

        Visit at : https://www.osttopstapp.com/split-vcf.html

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