Hi,

I am using Haplotype Caller to genotype a VCF file. I am using this exact command line:

java -Xmx20g -jar GATK/3.6-0-g89b7209/GenomeAnalysisTK.jar \
-T HaplotypeCaller -R $indexFasta -I $Bam -o output.snps.indels.g.vcf \
-dt NONE --genotyping_mode GENOTYPE_GIVEN_ALLELES \
--alleles $vcffile

For most of the cases, it genotypes everything fine but for one sample, it doesn't genotype 2 indels calls that are present in the "--alleles" VCF file.

These are the 2 variants it is missing:

CHROM POS ID REF ALT QUAL FILTER INFO

13 28608262 . T TTCATATTCTCTGAAATCCTGA 343 PASS DP=2682;AF=0.006711;SB=0;DP4=1317,1363,9,9;INDEL;HRUN=2
13 28608265 . A ATATTCTCTGACTTCG 6470 PASS DP=2712;AF=0.082227;SB=4;DP4=1220,1288,116,107;INDEL;HRUN=1

They both are close to each other so not sure if it cannot genotype it because these 2 indels are in such close proximity and overlapping each other. Do you have any suggestions on how this can be fixed.

Thank you.
abolia