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What With Variants For Chromosome Y (1000Genomes Phase 1 Release)?

Here the VCF files with variants from 1000genomes project are available: ftp://ftp.ncbi.nih.gov///1000genomes/ftp/release/20110521/

But what with chromosome Y? Why there is no file with variants for Y chromosome?

1000genomes variant vcf
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updated by Laura Laura • written by agnieszka • agnieszka

2 answers

From 1000 genome project website -

So far we only have pilot project snps for the Y and the MT chromosomes and these can be found in a_map_of_human_variation.

Also you can have look at this pdf.

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written by Vikas Bansal Vikas Bansal

We hope to release chrY calls for the phase1 release very shortly. chrY unfortunately is more difficult to call accurately than the autosomes as we have fewer individuals (about 50%) who are male so it takes longer to produce high quality results

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written by Laura Laura

chrY and chrMT variants are now available and can be found in ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/integrated_call_sets/

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written by Laura Laura

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