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hartwigmedical / hmftools

Various algorithms for analysing genomics data
GNU General Public License v3.0
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Problem running Lilac #545

Closed vaksmaz closed 2 months ago

vaksmaz commented 2 months ago

I ran a test command and ran into an issue, the error was as follows: This does not need the full error, it will be evident.

Exception in thread "main" htsjdk.samtools.SAMFormatException: SAM validation error: ERROR::INVALID_MAPPING_QUALITY:Record 2994, Read name A00404:238:H7W75DSXY:3:1464:1199:27398, MAPQ should be 0 for unmapped read. at htsjdk.samtools.SAMUtils.processValidationErrors(SAMUtils.java:457) at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:849) at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:834) at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:802) at htsjdk.samtools.BAMFileReader$BAMQueryFilteringIterator.advance(BAMFileReader.java:1079) at htsjdk.samtools.BAMFileReader$BAMQueryFilteringIterator.(BAMFileReader.java:1048) at htsjdk.samtools.BAMFileReader.createIndexIterator(BAMFileReader.java:959)

charlesshale commented 2 months ago

The BAM has invalid reads - in this case unmapped reads with a map qual > 0. There may be tools to correct this issue, otherwise we recommend using BWA for alignment as it does not result in these invalid reads.

Most of our tools can be run with BAM validation stringency turned to SILENT, but Lilac does not have this option. We will add it to the next release.