Germline variants from lancet

[gilhornung]

One last question regarding lancet...
Can I use the output in the VCF to extract germline variants (e.g. variants labelled HighVafNormal;HighAltCntNormal) or should I run another germline variant caller in parallel (e.g. HaplotypeCaller)? It seems to me that there shouldn't be a reason why to perform local assembly twice, but maybe I am missing something...

Thanks,

Gil

[gnarzisi]

Yes, you can use the germline variants reported by lancet. However, keep in mind that those are flagged as germline even when supported only by very few reads in the nromal (see default values for HighVafNormal, HighAltCntNormal, etc.)