Question: Merge phased files from ShapeIT
0
gravatar for nataliagru1
15 months ago by
nataliagru150
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!

NG

phasing shapeit • 377 views
ADD COMMENTlink modified 15 months ago by Charles Warden7.9k • written 15 months ago by nataliagru150
1
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
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1666 users visited in the last hour