Question

a question about HaplotypeCaller and skipping "indel realignment" and re-calibration" steps

0

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6.7 years ago

Siavash Salek Ardestani ▴ 20

Hi can I skip "indel realignment" and re-calibration" steps, when I am using HaplotypeCaller ?

SNP GVCF GATK • 1.6k views

ADD COMMENT • link updated 6.7 years ago by Devon Ryan 104k • written 6.7 years ago by Siavash Salek Ardestani ▴ 20

score 3 · Accepted Answer · 2018-03-23

3

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6.7 years ago

Devon Ryan 104k

InDel realignment you can skip. I think base quality recalibration is no longer in the GATK best practice, but you should double check that.

ADD COMMENT • link 6.7 years ago by Devon Ryan 104k