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Question: Mismatch penalty in BWA
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gravatar for Juan Ledesma
15 months ago by
Juan Ledesma • 0
United Kingdom
Juan Ledesma • 0 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 • 720 views
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modified 14 months ago • written 15 months ago by Juan Ledesma • 0
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gravatar for Jennifer Hillman Jackson
14 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 14 months ago by Jennifer Hillman Jackson ♦ 25k
0
gravatar for Juan Ledesma
14 months ago by
Juan Ledesma • 0
United Kingdom
Juan Ledesma • 0 wrote:

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

Juan
ADD COMMENT • link written 14 months ago by Juan Ledesma • 0
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