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Total Samples In 1000 Genomes Vcf File

Hi all, I wanted to know if someone was aware of how many exact number of samples are in the 1000 genomes VCF file?

Thanks in advance.

vcf 1000genomes
• 3,507 views • link
updated by donfreed donfreed • written by win win

2 answers

There are 1092 samples in the chromosome 1-23 VCF files from phase 1. The Y and MT chromosome VCFs had one or two sample IDs not among the 1092, iirc.

• 300 views • link
written by chrchang523 chrchang523 
grep '#CHROM' 1.1-50000.ALL.chr1.integrated_phase1_v3.20101123.snps_indels_svs.genotypes.vcf | awk '{print NF; exit}'

prints 1101. 1101-9 (for the other fields in the VCF) = 1092

• 115 views • link
written by donfreed donfreed 
bcftools view -h ALL.chr22.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz | grep "^#CHROM" | cut -f10- | awk '{print NF}'

just as an update, latest 1000genomes September 2014 release contains 2504 samples.

• 0 views • link
written by Jorge Amigo Jorge Amigo

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