[Bio-bwa-help] changing the clipping settings
Status: Beta
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From: Mulder, K. P. <Mu...@si...> - 2013-10-23 21:54:36
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Dear BWA community, I am using bwa mem and I have noticed that a lot of my reads are mapping onto my constructed reference with minimal overlap and the majority of the 150bp read clipped off (e.g. 50 base pair of good overlap and 100 base pair clipped). I want bwa to throw these reads out and not map them. Increasing the clipping penalty does not work as I believe this only affects the question of clipping vs allowing mismatches as the read is already seeded. I want something along the lines of: if more than 75basepairs need to be clipped do not map the read at all. The only parameter that i feel could do that is to increase the seed length to 75bp but I do not think that is the best way to do it. Are there other options within BWA to do so? Or should i somehow do this with a post mapping processing step? My command is: bwa mem -v 3 -t 1 -R '@RG\tID:21PC10\tSM:PC10\tPL:ILLUMINA REF.fasta read01.fastq read02.fastq > name.sam Thank you for your time! Any help or idea is appreciated! Kevin |