Question: bwa mem -T (alignment score) not doing anything
gravatar for chris.bird
3 months 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 • 172 views
ADD COMMENTlink written 3 months 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 3 months ago by ATpoint7.5k
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