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Question: how to relate BWA input parameters to get minimum coverage and identity
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gravatar for gm
15 months ago by
gm • 0
gm • 0 wrote:

Hi all and thanks in advance for any help you will kindly provide.

I'm aligning some short sequences against a few databases by means of BWA. I need to recover bot identity and coverage in a fast way at the end of the alignemnet. I read that I can use the M field in CIGAR form SAM and further parameters from SAM to distinguish between match/mismatch. Can you give more precise information on this point?

Is there easy way to modify BWA to have identity and coverage directly (as it is done in DeconSeq, whose code I tried to analyse but with little success)?

Is there any settings for input parameters to BWA to obtain some desired coverage and identity?

Thanks a lot, Giovanna

alignment • 471 views
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modified 15 months ago • written 15 months ago by gm • 0
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gravatar for Jennifer Hillman Jackson
15 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

There isn't a public tool (that I am aware of) that takes an input BAM/SAM dataset and then outputs per-query-read-alignment percent identity and coverage.

BWA has many options for filtering alignments. Open up the advanced settings to review. These options correspond to the same options found in the BWA manual.

Another choice is to post-alignment filter your current results. Try these two first: Filter mapped reads on MD tag string or BAM filter?

Thanks! Jen, Galaxy team
ADD COMMENT • link written 15 months ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for gm
15 months ago by
gm • 0
gm • 0 wrote:

Thanks for your kind support. I'll have a try.
ADD COMMENT • link written 15 months ago by gm • 0
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