Question

Sequence Haplotypes From 1Kg Project Variants

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11.8 years ago

Zev.Kronenberg 12k

Greetings,

I need to create haplotype sequences (fastas) from the 1000 genomes data. I was wondering if anyone knows of a tool before I start writing my own?

I want to be able to pass in hg19 coordinates & 1kg.vcf & hg19.fasta and reconstruct all the haplotypes for that region.

1000genomes haplotype vcf • 2.7k views

ADD COMMENT • link updated 11.8 years ago by Peixe ▴ 660 • written 11.8 years ago by Zev.Kronenberg 12k

score 6 · Answer 1 · 2013-02-04

6

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11.8 years ago

Adam ★ 1.0k

VCFtools should be able to do this:

cat ref.fa | vcf-consensus file.vcf.gz > out.fa

ADD COMMENT • link 11.8 years ago by Adam ★ 1.0k

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Do you know if this supports multiple individuals? I don't want it to collapse the individuals into a consensus .

ADD REPLY • link 11.8 years ago by Zev.Kronenberg 12k

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I haven't used it for this, but it does have a --sample argument that sounds like it will do what you want.

ADD REPLY • link 11.8 years ago by matted 7.8k

score 2 · Answer 2 · 2013-02-04

Take a look at Plink options for working with haplotypes here. I have been recently using it quite a lot for some haplotype calculations, and sounds like it might work for what you want, if you specify the haplotypes. But I don't know if sequences as large as fasta are gonna be accepted. Anyway looking is free, and the plink tutorial is really good! ;)

Cheers!