How can I get an allele count table from a .vcf file?
What's the most efficient way to generate a table of allele counts from a .vcf file? Ideally columns Chrom, Position, ref counts, and alt counts, across all sites in a vcf file? I think what I'm looking for is basically CollectAllelicCounts from GATK but on a vcf rather than bam file. Thanks.
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Jeremy Leipzig
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mrk •
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mrk •
3 answers
$ bcftools stats in.vcf.gz | grep -wF ST
# ST, Substitution types:
# ST [2]id [3]type [4]count
ST 0 A>C 5
ST 0 A>G 5
ST 0 A>T 3
ST 0 C>A 5
ST 0 C>G 2
ST 0 C>T 0
ST 0 G>A 1
ST 0 G>C 4
ST 0 G>T 2
ST 0 T>A 4
ST 0 T>C 4
ST 0 T>G 5
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Pierre Lindenbaum
With plink2:
plink2 --vcf in.vcf.gz --freq counts cols=chrom,pos,ref,alt,reffreq,altfreq
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chrchang523
With TileDB-VCF (where uri is a TileDB-VCF dataset)
tiledbvcf.read_allele_frequency(uri, region=None)
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Jeremy Leipzig
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