The current GATK version is 3.5-0

#### Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

# Indel Calling

Posts: 6Member

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.

Tagged:

Hi there,

Is your indel quite big? If so you may need to use HaplotypeCaller and override the default ActiveRegion size to increase the callable size.

You can also try running in GENOTYPE_GIVEN_ALLELES mode to force a call.

Geraldine Van der Auwera, PhD

• Posts: 6Member

Thank you Geraldine. I will give this a try. The indel is just a dupT.

• Posts: 6Member

Geraldine,

I used these parameters for UnifiedGenotyper and received no variants and no input indel vcfs for the indel realignment step.

-stand_call_conf 30.0 -stand_emit_conf 0.0 --min_base_quality_score 0 -glm BOTH --dbsnp $dbSNPRef -nt$numThreads -rf BadCigar -minIndelCnt 3 -minIndelFrac 0.15 --genotyping_mode GENOTYPE_GIVEN_ALLELES

I'm obviously missing something. It appears that I should have included the --alleles flag. What should I be passing to the --alleles flag? I don't quite understand RodBinding[VariantContext]. Could I pass a bed file for regions which I want to force a call, so that I can then go back and see what kind of quality scores prevented the dupT from being called in the first place?

Thank you.