Question: liftover not giving same number of columns
gravatar for GK1610
7 months ago by
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

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
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