I am using BWA for mapping. My main objective is to call polymorphisms from my genome resequenced data for two different populations for a plant model which has its reference genome sequenced.
If there are reads that align to multiple regions mainly from the paralogs (from duplicate genes/genomic regions, not for other repetitive regions) is it possible to make the read only align to the best match rather than matching it to two different places. - I want the polymorphism information at coding region not to be ambiguous although sequence error might contribute some mis-matching which I think will be less.
If I want to call variant on the alignments (SAM/BAM) which caller is best that will account for multiple mapped reads when scoring variants.
Thanks in advance !