I tried two uncover the genetic structure for a bird population using resequencing data, with PAIRED-END 100 bp reads. I used two different mapping methods BWA mem and BWA aln, and then used SAMtools to get vcf file. After filtering, we get two different SNP datasets when using BWA mem and BWA aln, and of course, this leads to two diffrent genetic structures for the same population! The problem is the mapping methods BWA mem and BWA aln, which one should I trust?
Any suggestions would help a lot! My best wishes, Dezhi