I'm using pindel on a set of sample pairs aligned using bwa mem but it doesn't make a good usage of the specified threads. In addition it seems to take too long to process a single chromosome. When I run pindel on the same samples but aligned using bwa aln the profile of multithreaded usage is completely different and much more efficient.
Is it possible that pindel doesn't make a good usage of the new flags in the bam reported by bwa mem, since now it's possible to find multiple primary alignments for a split read and the new supplemental flag 0x800?
A typical call to pindel is:
pindel-0.2.5a3 -f /path/to/hg19.fa -i /path/to/config.txt -o my_sample -c Y -T 8
Also mention that the argument -M
was not set in the alignment of the samples with bwa mem.
Best,
Xavier
I'd just like to mention that after removing the supplemental reads in the bwa mem alignment (samtools view -bh -F 0x800) pindel seems to behave similar as to bwa aln alignments, at least computationally. I still need to confirm how about the final results.
If this is true I guess my initial suspicion was true and pindel cannot deal well with bam files reporting several primary alignments for the same read.
Best,
Xavier