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OverclippedReadFilter doesn't filter anything
I have 51bp reads and am trying to filter out those where about 20-30 bases have been soft-clipped. The command I have been using is:
java -Xmx8g -jar $GATK_JAR -R $REFERENCE -T PrintReads -rf OverclippedRead --filter_is_too_short_value 40 -o /dev/stdout --disable_bam_indexing -I snippet.bam
Using GATK version v3.4-46, human reference hg19.
The problem I'm encountering is that this doesn't actually filter out any reads. I'm looking at many reads with 27 soft-clipped bases and 24 matches, but those are included in the output. Also the log is unambiguous:
-> 0 reads (0.00% of total) failing OverclippedReadFilter
MicroScheduler - 0 reads were filtered out during the traversal out of approximately 2474 total reads (0.00%)