Question: liftover not giving same number of columns
0
gravatar for GK1610
7 months ago by
GK161060
United States
GK161060 wrote:

I have a WGS file of 200 individuals. The file was aligned using hg19. I want to run liftover to change the coordinates to hg38

I am using vcf-liftover from here https://github.com/wtsi-team144/VCF-liftover

cat $my_wgs_vcf_file | vcf-liftover hg19ToHg38.over.chain.gz > output.vcf

the output.vcf from this file always gives me 63 individuals where 127 columns of individuals information gets lost.

Can you help with this?

snp genome • 249 views
ADD COMMENTlink written 7 months ago by GK161060
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: 1494 users visited in the last hour