Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Haplotype Caller Makes SNPs look like INDELS
I'm using the HaplotypeCaller to look at SNPs related to antimicrobial resistance and am getting a result that looks like this:
NC_011035.1 2049708 . CCGGCG C ... NC_011035.1 2049714 . C CAAGAA ...
I believe this is an alignment that would look like:
but instead of giving me 5 individual SNPs, GATK is calling the region as though it is a 5bp deletion at position 2049708 and a 5bp insertion at position 2049714.
Is there any way to change the parameters so that the appropriate call is made?
My current command is:
java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -nct 12 -R NCC_011035.fasta -I ST547_dedup_reads_group.bam --genotyping_mode DISCOVERY -stand_emit_conf 10 -stand_call_conf 30 -o ST547_raw.vcf