Dear GATK Team,
I am following the guidelines in the following documentation for data preprocessing: Data pre-processing for variant discovery and (How to) Map and clean up short read sequence data efficiently.
Picard version: 2.23.8. GATK version: 188.8.131.52.
When processing the output BAM after running ApplyBQSR through ValidateSamFile, I am receiving the following error:
## HISTOGRAM java.lang.String
Error Type Count
However, I confirm the BAM showed no errors with ValidateSamFile prior to running BaseRecalibrator and ApplyBQSR and both BaseRecalibrator and ApplyBQSR ran successfully. FixMateInformation does not resolve this issue.
Why do I see a new error in the BAM after running BQSR? Could it be due to the default read filters differing between BaseRecalibrator and ApplyBQSR or alternatively, another read filter being required?
Thank you for your time and help.
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