How many samples are there in 1000 genome project VCF file?
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5.5 years ago
MAPK ★ 1.9k

Although my question is kind of silly, I have downloaded the VCF file from 1000genome project website and it looks like the VCF files only include 436 samples. Can someone please direct me to the VCF files with all 1000 samples. Thanks

vcf 1000genome • 1.8k views
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I wonder if it has to do with the phase of the 1000 genomes project. Each phase had different numbers of individuals sequenced (i.e. Pilot: 179 individuals, Phase 1: 1,092 individuals, Phase 3: 2,504 individuals) although the number 436 is not in either of those. Can you point us to the link you downloaded the data from please?

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I just talked to Susan Fairley (1000Genomes team) about this. Please email the 1000 Genomes team if you want to discuss this further.

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Hi Denise, This is where I downloaded the files from: http://www.1000genomes.org/announcements/complete-genomics-data-release-2013-07-26/

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Have you checked the Checksum files? it could be that during downloading the files were truncated!

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5.5 years ago

Here you can find a list of all their VCFs and samples available:

http://www.1000genomes.org/data

http://www.1000genomes.org/data-portal/sample

1000 Genomes Project

1000 Genomes Release Variants Individuals Populations VCF Alignments Supporting Data

Phase 3 84.4 million 2504 26 VCF Alignments Supporting Data

Phase 1 37.9 million 1092 14 VCF Alignments Supporting Data

Pilot 14.8 million 179 4 VCF Alignments Supporting Data

Your VCF is probably only with the samples from Complete Genomics!

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Thanks, you are right. They are only from Complete Genomics.

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