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

Question

[agnieszka]

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?

Answer 1

[Vikas Bansal]

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.

[Laura]

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

Answer 2

[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/