Dear GATK team,
I have a large reference database (NCBI nt) and it's to big to index. I split it to smaller partial dbs and run my alignment tool against each of the partial dbs separately. So for 1 file with reads I get bunch of sam/bam files with alignments to partial reference. Now I want to merge my result sam/bam files properly with no duplicates and (ideally) recalculate the mapq scores. Is there any tool which could help me with part of the task at least? samtools merge doesn't seem applicable, it produces lots of duplicates. BTW, I'm interested only in mapped reads.
Thank you,
Yulia