After aligning data using the presplit_map.py Python script, the next recommended step is to use Picard FixMateInformation and MarkDuplicates. However, using the current version of Picard I get
Exception in thread "main" htsjdk.samtools.SAMFormatException: SAM validation error: ERROR: Record 1, Read name K00280:111:HWNMLBBXX:7:1101:1174:14643, Mapped mate should have mate reference name
Which is hogwash:
$ samtools view 1-1.bam | head -n 4 | cut -f 1-2 K00280:111:HWNMLBBXX:7:1101:1174:14643 81 K00280:111:HWNMLBBXX:7:1101:1174:14643 145 K00280:111:HWNMLBBXX:7:1101:1174:14713 2049 K00280:111:HWNMLBBXX:7:1101:1174:14713 81
Anyway, is there some trickeration that needs to be done (other than using VALIDATION_STRINGENCY=DONTBOTHERMEABOUTFAKESTUFF)?