I am using the newer version of the threespine stickleback genome, where the authors were able to add the chrY to the reference. In their paper they've used bowtie2 to test the alignments and it works (I've tested myself too). However, I cannot get reads to align to the chrY using BWA (v.0.7.17). I'm following the GATK best practices and checked to see if that would be an issue after MarkDuplicates, but the result is the same before the marking. The command that I'm using to run BWA is:
bwa mem -M -p
Do you think the -M command would have anything to do with that? I would appreciate any light into this issue! Thank you.
Hello,
I am using the newer version of the threespine stickleback genome, where the authors were able to add the chrY to the reference. In their paper they've used bowtie2 to test the alignments and it works (I've tested myself too). However, I cannot get reads to align to the chrY using BWA (v.0.7.17). I'm following the GATK best practices and checked to see if that would be an issue after MarkDuplicates, but the result is the same before the marking. The command that I'm using to run BWA is:
bwa mem -M -pDo you think the -M command would have anything to do with that? I would appreciate any light into this issue! Thank you.