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--dontUseSoftClippedBases option seems to involve non-softclipped bases


I am checking the differences between the calls with/without using soft clipped bases.
Some of the missed calls when '--dontUseSoftClippedBases=true' (compared with the calls when 'false') harbored in the middle of the reads, not in the soft-clipped bases.
Why the calls were missed?
Many thanks!!


  • AdelaideRAdelaideR Unconfirmed, Member, Broadie, Moderator admin

    Hello @ensel

    There may be one or two reasons why this is happening. There is an informative discussion on the forum here.

    The reads may have low DP or MQ in that particular area.

    Also, Haplotype caller has a realignment step after identifying active regions that recalculates the DP, so some calls may be rejected after this step.

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