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VDBWRAIR / ngs_mapper

Genome Mapping Pipeline
GNU General Public License v2.0
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Mapped Read Count #272

Open averagehat opened 6 years ago

averagehat commented 6 years ago

Right now the pipeline seems to include chimeric/supplementary reads in its read count. This is consistent with bwa output. But the result is that unmapped+mapped =/= total reads.

http://seqanswers.com/forums/showthread.php?t=32708

Maybe we should change bwa settings or filter the bam file.

averagehat commented 6 years ago

samtools view -F 2048 https://broadinstitute.github.io/picard/explain-flags.html