Question: Merge phased files from ShapeIT
gravatar for nataliagru1
15 months ago by
nataliagru150 wrote:

Dear all,

I have used ShapeIT to phase several VCF files. Each vcf file corresponding to a chromosome since ShapeIT can only phase when the data is separated by chromosome.

I now have outputted phased data for each chromosome as such trypanosome_chr1.phase, trypanosome_chr2.phase, etc.

I am wondering if there is now a way to merge these phased files together and have one .phase file that contains data for all chromosomes!

I hope this makes sense!!

Thank you very kindly any help would be greatly appreciated!


phasing shapeit • 377 views
ADD COMMENTlink modified 15 months ago by Charles Warden7.9k • written 15 months ago by nataliagru150
gravatar for Charles Warden
15 months ago by
Charles Warden7.9k
Duarte, CA
Charles Warden7.9k wrote:

If your downstream program (like RFMix) also processes each chromosome separately, perhaps you want to wait on the merging step.

I might have had other reasons to want to use a custom script to parse / join / filter .vcf files, but perhaps you could give vcftools a try?

ADD COMMENTlink written 15 months ago by Charles Warden7.9k
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