I have a set of bam files obtained by using bowtie1 as aligner. I want to use GATK's current version for carrying out snp calling.
When I run GATK's current version of snp calling, I get this error
Looking more carefully at the bam files, I noticed that 5th column has 255 as quality score which means mapping quality unavailable.
Going through blogs I came across this post where reverting back to a previous version of GATK fixed the issue
Now bowtie always produce quality score of 255.
I am interested in using current GATK version for snp calling. The version used above in the post is very very old. Is there a way i can modify the existing bam files obtained from bowtie so that i can use it with current GATK version of snp calling.
PS: Ofcourse i can map the reads with bwa
Hope to hear from you soon