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!