1bp deletion (Sanger confirmed) not called with HaplotypeCaller and UnifiedGenotyper
Dear GATK Team,
I have encountered a problem while doing a variant calling. I received raw reads from sequencing company and wanted to do some analysis myself. I did everything according to GATK best practices and everything was fine until I looked at VCF file for called variants and I did not find the variant which was reported to me from sequencing company as a disease causing mutation and therefore was the only one I especially searched for. It is a 1bp heterozygous deletion, which can be seen in IGV picture attached to this post. I have tried to change parameters for both HaplotypeCaller and UnifiedGenotyper, but nothing has made them to call this indel.
The last command I used was:
java -jar ~/NGS_programs/GenomeAnalysisTK-2.8-1-g932cd3a/GenomeAnalysisTK.jar -T UnifiedGenotyper -R ~/NGS_data/hg19/ucsc.hg19.fasta -I KO002_P.merged.dedup.realn.bam -stand_call_conf 20 -stand_emit_conf 1 -L chr6:157097064-157533913 -o ARID1B/ARID1B_UG_emit1_call20_INDEL.vcf -glm INDEL
I also have tried lowering the -minIndelCnt, -minIndelFrac arguments, and maximized the --max_deletion_fraction while using UG. But nothing helped.
Do you have any ideas what could be the problem?
Thank you in advance!