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Variant missing call

Dear GATK team,

We are doing a variant calling from an alignment done by BWA-MEM, in our proof of concept we expect to find a variant. The variant is after an homopolymeric region (13A). When we look at the alignment with the IGV, the variant is clearly present as you can observe in the image attached, but when we do the variant calling by GATK with the command below, the variant is not reported. How can we modify the filtering to solve this problem? Any hint?

Thank you very much in advance. Regards,

Adriana

/usr/java/latest/bin/java $RAM \
-jar ${GATK}/GenomeAnalysisTK.jar -nt $CORES \
-R ${ref_hg19}/ucsc.hg19.fasta \
-T UnifiedGenotyper \
-I ${file} \
-o ${vars_raw}/${file_res} \
--genotype_likelihoods_model BOTH \
-stand_call_conf 30 \
-stand_emit_conf 30 \
--max_alternate_alleles 6 \

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