We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

Choice of Known indels file for local realignment

Dear all:

I am following a pipeline in an article to realign WGS reads to GRCh38 in an ALTs aware manner. I plan to use gatk 3.7 to do the local realignment.
I am wondering is it OK to use "Homo_sapiens_assembly38.known_indels.vcf.gz" on the google cloud bucket as a known indels file for local realignment with "IndelRealigner"?
And is this the 1000 genome phase3 known indels file?

I know that gatk4 no longer does realignment. But I still need to do it. I am just confused about which known indels file to use, since I want to process reads re-aligned to GRCh38.

Many thanks,
Yidong Zhang
Sign In or Register to comment.