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Count SNPs per individual FAST!

Say I have a large (N samples > 2000) VCF or plink bed file.

What's the quickest way to calculate the number of alleles (unique alleles and # ALT genotypes) for each sample?

What are the options that can quickly digest a 1Tb VCF (broken by chrom)?

Plink is ridiculously fast for this, but I don't think it can perform a per-sample count of variants

plink snp gwas
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updated by chrchang523 chrchang523 • written by QVINTVS_FABIVS_MAXIMVS QVINTVS_FABIVS_MAXIMVS

in the title you want to count the number of snp per individual, in the body you want the number of allele for each sample. Please, show us the expected output.

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written by Pierre Lindenbaum Pierre Lindenbaum

Either

IID    #UNIQUE_ALLELES

Or

IID   #UNIQUE_ALLELES    #ALT_ALLELES

so the first file would output ID1 1 for 1/1 genotype but the second file you have ID1 1 2

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written by QVINTVS_FABIVS_MAXIMVS QVINTVS_FABIVS_MAXIMVS

1 answer

plink --score can be abused for this purpose.

  • Create an input file assigning weight 1 to every alt allele to get #ALT_ALLELES.
  • You can then repeat the --score computation after erasing all the heterozygous calls ("plink --set-hh-missing --chr-set -26 --make-bed"; it may be necessary to use "--output-chr 26 --make-bed" first to force numeric chromosome codes). You should be able to infer #UNIQUE_ALLELES once you have both --score output files.
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written by chrchang523 chrchang523

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