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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