Frequently Asked Questions

Is Jacquard a variant caller?

Jacquard is not a variant caller. It accepts VCF output from variant callers and integrates them for simplified annotation and analysis.

Can Jacquard annotate data?

No, Jacquard cannot annotate data; however the output from translate, merge, and summarize can be run through an annotation tool such as SnpEff or Annovar.

Can I use Jacquard with any variant caller?

Merge and expand are able to process VCF files from any variant caller. Translate and summarize, however, must be run with VCF files from one or more of the supported variant callers. Currently, Jacquard supports MuTect, VarScan, and Strelka.

I’d like to merge my VCFs, but my caller isn’t supported by Jacquard.

Both merge and expand commands can be used to show all of the results from different callers without standardization of the input data. However, it is recommended that the input data be standardized whenever possible to directly compare data across callers.

Does Jacquard work with germline callers?

The translate command is optimized to work with tumor-normal sample pairs. Germline VCFs can be used with merge and expand commands. Better support for germline and pedigree VCFs is coming soon.

Still Have Questions?

Email bfx-jacquard@umich.edu for support and questions.