Question: convert vcf file (based using beagle) to ldhat input files when I have 6000 "chromosomes" (scaffolds)
0
gravatar for jc_jones
4 days ago by
jc_jones0
jc_jones0 wrote:

I am hoping to use vcftools to convert my phased vcf file (from beagle, where the genotypes are coded as reference and alternate - 0 and 1) into the format required for LDhat.

This is possible using the —ldhat flags, however I want to include all of my “chromosomes” (scaffolds) of which there are around 6000. Do I need to include a list of all 6000 chromosomes? Or how can I use vcftools to convert to LDhat format in my case?

Also, is it possible to convert the 0s and 1s to the actual nucleotides, as required for LDhat?

Many thanks for any help or suggestions,

Julia

ldhat format vcftools • 57 views
ADD COMMENTlink modified 4 days ago • written 4 days ago by jc_jones0
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: 1265 users visited in the last hour