I have Ion Torrent data. I am trying to call a variant that I know to exist (confirmed with Sanger). In the position where there is the known indel, I have a depth of roughly 80-90 (in two different runs) and a of those between 20-23% of the reads have the insertion called. What parameters should I be adjusting to get this indel to call? I don't mind a large number of false positives.
I've tried several iterations that include indel realignment using known indels (1000G_phase1 and ills_and_1000G_gold_standard) and also excluding them. I have also tried iterations of setting these flags in UnifiedGenotyper:-stand_call_conf 30.0 -stand_emit_conf 0.0 --min_base_quality_score 0 -glm BOTH --dbsnp dbsnp_137.b37.vcf -nt -rf BadCigar -minIndelCnt 3 -minIndelFrac 0.15. I have also attempted to use HaplotypeCaller: -stand_call_conf 30.0 -stand_emit_conf 0.0 --dbsnp dbsnp_137.b37.vcf -rf BadCigar
Any suggestions would be great.