Question: Comparing VCFs constructed from mapping to different reference genomes
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gravatar for kwalter
9 months ago by
kwalter10
kwalter10 wrote:

Hi, I am comparing variant calling pipelines from two authors who have used different versions of a reference genome. Is there a tool that could allow me to compare VCF files constructed from mapping/variant calling on two different ref genomes? Or is there a method for converting the VCF to a VCF from a different ref genome?

Thank you in advance for your help!

ADD COMMENTlink modified 9 months ago • written 9 months ago by kwalter10
0
gravatar for kwalter
9 months ago by
kwalter10
kwalter10 wrote:

I am responding to my own question above. I have found a Picard tool

https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.0.0/picard_vcf_LiftoverVcf.php that looks like it would allow me to "lift over" my variants onto another genome build.

Thanks!

ADD COMMENTlink written 9 months ago by kwalter10
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