optimize a execution of a pindel process

[cmccabe]

I am looking to optimize a pindel process. Below is the command used:

pindel -f refererence -i configfile -c ALL -T 16 -o sample

I then execute pindel2vcf on the output.... I was thinking of adding

samtools view -h -F 0x900 <bam>

before making the configfile to filter or secondary and supplementary alignments. My thinking is that pindel will be able to use the primary alignments better without these other alignments slowing it down, is that true or is there a better option? Thanks