Hi,
I am using BWA-SW for the alignment of 454 amplicons and later detection of variants. When I do my proof of concept, I find that if the variant is in 2nd bp 3' or 5', BWA-SW does't map 1st and 2nd bases so variant caller doesn't find the variant.
Could anyone help me with the parameters should I use? By the moment I am using this command:
./bwa bwasw -a 1 -b 3 -q 3 -r 1 -d 0 ${ref} $files/file.fq > ${alignments}/file.sam
Thank you very much in advance! Any hint will be usefull!
I am using BWA-SW for the alignment of 454 amplicons and later detection of variants. When I do my proof of concept, I find that if the variant is in 2nd bp 3' or 5', BWA-SW does't map 1st and 2nd bases so variant caller doesn't find the variant.
Could anyone help me with the parameters should I use? By the moment I am using this command:
./bwa bwasw -a 1 -b 3 -q 3 -r 1 -d 0 ${ref} $files/file.fq > ${alignments}/file.sam
Thank you very much in advance! Any hint will be usefull!
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