Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
Here REF is the reference genome, and NAME is the name of the sample. Each interval is one gene. With these parameters it takes around 3-4 min for each interval on a 64GB machine.
I was wondering if there was a possibility of speeding up the process ( other than reducing -x or increasing -T ). Is there something I might be missing ?
Hi, I am using Pindel 0.2.5b9, and using the following command :
$pindelsoftwareDIR/pindel -f $REF -i $NAME".pindel.txt" -c $interval -o $cnvsDir/$NAME.$interval -x 8 -T 12 -L $cnvsDir/$NAME.$interval.pindel.log
Here REF is the reference genome, and NAME is the name of the sample. Each interval is one gene. With these parameters it takes around 3-4 min for each interval on a 64GB machine.
I was wondering if there was a possibility of speeding up the process ( other than reducing -x or increasing -T ). Is there something I might be missing ?
Thank you, Debayan