Opened 23 months ago
Closed 23 months ago
#1440 closed enhancement (fixed)
Add option for running Picard MarkDuplicates with -VALIDATION_STRINGENCY LENIENT parameter
Reported by: | Nicklas Nordborg | Owned by: | Nicklas Nordborg |
---|---|---|---|
Priority: | major | Milestone: | Reggie v4.41.4 |
Component: | net.sf.basedb.reggie | Keywords: | |
Cc: |
Description
The BAM file produced by the Hisat/2023 pipeline contained an entry with a strange CIGAR string 46M2D13M13I1D2I31M
that Picard exits with an error when running the MarkDuplicates step:
SAM validation error: WARNING::ADJACENT_INDEL_IN_CIGAR:Read name A01932:18:HH3GJDRX2:1:2269:23592:30733, No M or N operator between pair of I operators in CIGAR
It is possible to ignore this by adding -VALIDATION_STRINGENCY LENIENT
to the command line.
This can be solved by adding an extra configuration in reggie-config.xml
under a named parameter-set
, and use a Software item that selects this parameter set. The Software item should NOT be a default software since we always want to try without the LENIENT parameter first.
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