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!

Running HaplotypeCaller on a multi-lane sample


I am interested in running HaplotypeCaller for a multi-lane sample. What is the best way to do this? I followed the protocol here (https://software.broadinstitute.org/gatk/documentation/article?id=6057) which states to run MarkDuplicates and BQSR before HaplotypeCaller, which I did. I fed the new BAM file into HaplotypeCaller but get an error with a corrupt gVCF file. Am I meant to merge the read groups into a single read group before using HaplotypeCaller?


Sign In or Register to comment.