Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

Should I use UnifiedGenotyper or HaplotypeCaller to call variants on my data?

Geraldine_VdAuweraGeraldine_VdAuwera Posts: 5,213Administrator, GSA Member admin

The HaplotypeCaller is a more recent and sophisticated tool than the UnifiedGenotyper. Its ability to call SNPs is equivalent to that of the UnifiedGenotyper, and its ability to call indels is far superior. We recommend using HaplotypeCaller in all cases, with only a few exceptions:

  • If you want to analyze more than 100 samples at a time (for performance reasons)
  • If you are working with non-diploid organisms (UG can handle different levels of ploidy while HC cannot)
  • If you are working with pooled samples (also due to the HC’s limitation regarding ploidy)

In those cases, we recommend using UnifiedGenotyper instead of HaplotypeCaller.

Geraldine Van der Auwera, PhD

Comments

Sign In or Register to comment.