Hi GATK team,

it's not a problem with gatk (currently 4.1.5.0) but with a bam  processed with bwa but containing a few reads with a cigar string starting with a Deletion.

<pre>

org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 2.56 minute

s.
Runtime.totalMemory()=176910336
***********************************************************************

A USER ERROR has occurred: Read V1:1:HN23NDSXX:4:1405:32931:18380 chr1:5374345-5374396 is malformed: read ends with deletion. Cigar: 65H48M3
8I4D. Although the SAM spec technically permits such reads, this is often indicative of malformed files.

***********************************************************************
org.broadinstitute.hellbender.exceptions.UserException$MalformedRead: Read V1:1:HN23NDSXX:4:1405:32931:18380 chr1:5374345-5374396 is malform
ed: read ends with deletion. Cigar: 65H48M38I4D. Although the SAM spec technically permits such reads, this is often indicative of malformed
files.
at org.broadinstitute.hellbender.utils.locusiterator.AlignmentStateMachine.stepForwardOnGenome(AlignmentStateMachine.java:242)
at org.broadinstitute.hellbender.utils.locusiterator.PerSampleReadStateManager.updateReadStates(PerSampleReadStateManager.java:188)
at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.updateReadStates(ReadStateManager.java:118)
at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:318
)
at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:225)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils.getPileupsOverReference(AssemblyBasedCallerU
tils.java:443)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel.calculateRefConfidence(ReferenceConfidenceMo
del.java:195)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.callRegion(HaplotypeCallerEngine.java:645)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller.apply(HaplotypeCaller.java:212)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:200)

</pre>

My qestion is:

1) is it worth wrtiing a custom ReadFilter https://gatk.broadinstitute.org/hc/en-us/articles/360035532092-Read-filters ? I mean is the filter evaluated before or after the stepForwardOnGenome method above ?

2) If I write this custom IgnoreMalformedCIgarReadFilter what is the best way to include it in the classpath of gatk ,

Thank you for you help ?