Sequence Haplotypes From 1Kg Project Variants

Question

[Zev.Kronenberg]

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.

Answer 1

[Adam]

VCFtools should be able to do this:

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

[Zev.Kronenberg]

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

[matted]

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

Answer 2

[Peixe]

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!