Hi to all
can I skip "indel realignment" and re-calibration" steps, when I am using HaplotypeCaller ?
Skip indel realignment but include bqsr.
If you are working with small panels consists of not more than 100 or so genes you may also omit BQSR.
BQSR is not necessary for single amplicon or small panel data since there won't be enough data to generate a recalibration model.
Yes, we recommend BQSR. It is part of the Best Practices and to use an analogy from @Geraldine_VdAuwera, it is akin to purchasing fire insurance that prevents your house from burning down.
no I am working with whole genome sequence data. so is it necessary to using BQRS ?
Thank you so much.