Question: Mismatch penalty in BWA
0
gravatar for Juan Ledesma
11 months ago by
United Kingdom
Juan Ledesma0 wrote:

Hi

Does anyone know the highest mismatch penalty that I can set to get a more selective alignment in BWA?

I would like to map my reference sequence only to the reads that are identical and exclude those ones that can be similar but no identical to the reference sequence.

I am trying to identify the reads belonging to two genotypes in a sample even if both are very similar.

Thanks

bwa alignment mapping • 544 views
ADD COMMENTlink modified 11 months ago • written 11 months ago by Juan Ledesma0
0
gravatar for Jennifer Hillman Jackson
11 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

This prior post contains setting for finding hits with no internal mismatches. https://www.biostars.org/p/132681/

The advice to remove reads with unaligned ends (not fully contained within the central alignment) through filtering is a good if you want to do that as well. There are a few tools that can filter BAM datasets - search in the tool panel with the keywords "bam filter". Your target is the CIGAR string.

Line command arguments map directly to those on the Galaxy wrapper's tool form.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 11 months ago by Jennifer Hillman Jackson25k
0
gravatar for Juan Ledesma
11 months ago by
United Kingdom
Juan Ledesma0 wrote:

Thanks for your comments Jen, it is very useful for me. Cheers

Juan

ADD COMMENTlink written 11 months ago by Juan Ledesma0
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