Question: bwa mem -T (alignment score) not doing anything
gravatar for chris.bird
11 days ago by
chris.bird0 wrote:

I'm trying to control which reads are mapped to a reference genome by adjusting the the -T parameter in bwa mem, which is the minimum acceptable alignment score. The only problem is that reads with an alignment score below the threshold are being mapped anyway. I can see this when using samtools view to visualize the bam file, reads with an AS value less than the threshold are there. My data is paired end, so I tried doubling the threshold to account for both reads, but that didn't work either.

What's going on here? Do some settings in bwa mem interfere with -T?

snp sequence genome • 96 views
ADD COMMENTlink written 11 days ago by chris.bird0

For things like this, please give the version of BWA, full command line, the reference genome and an example of the problematic reads.

ADD REPLYlink written 11 days ago by ATpoint4.4k
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