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genome / bam-readcount

Count bases in BAM/CRAM files
MIT License
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Filteriing paired end data #45

Closed ktroule closed 7 years ago

ktroule commented 7 years ago

Hi

I'm using bamreadcount output as input for pVACseq. The thing is that I'm using paired end data from DNA and RNA, and I warnings like:

WARNING: In read XXXXXXXXXXXXXXXXXX: Couldn't find single-end mapping quality. Check to see if the SM tag is in BAM. I'm filtering using the parameter -b 20.

I'm not sure how this is affecting the filtering. I'm guessing the filtering by quality position is not being affected by this. But, What would happen if I was filtering instead by -b but by -q?

Thanks for your time.

ernfrid commented 7 years ago

It won't affect filtering at all. It will only affect the calculation of the avg_se_mapping_quality field.

ktroule commented 7 years ago

Thanks for this fast answer!