Merge phased files from ShapeIT

Question

[nataliagru1]

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

Answer 1

[Charles Warden]

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?