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Mapped Read Count #272

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averagehat opened this issue Nov 13, 2017 · 1 comment
Open

Mapped Read Count #272

averagehat opened this issue Nov 13, 2017 · 1 comment

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

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@averagehat