Merge phased files from ShapeIT
1
0
Entering edit mode
21 months ago
nataliagru1 ▴ 60

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

ShapeIT Phasing • 535 views
ADD COMMENT
1
Entering edit mode
21 months ago

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 COMMENT

Login before adding your answer.

Traffic: 1398 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6