A similar problem has been reported before, however couldn't solve for my case---
I ran the following command on a 2 sample set with GATK latest and GATK-3.6.0 to combineGVCF files for the contig hs37d5
../bin/gatk-18.104.22.168/gatk CombineGVCFs -R /scratch/HS_Build37/BWA_INDEX_hs37d5/hs37d5.fa -V IPF0047.194173.endPosCorr.gvcf.gz -V IPF0048.194174.endPosCorr.gvcf.gz-L hs37d5 -O cohort.2.3.newGATK.hs37d5.gvcf
java -jar /nfs/goldstein/software/GATK/GATK-3.6.0-ArchivedVersion-g89b7209-patched/GenomeAnalysisTK.jar -T CombineGVCFs -R /scratch/HS_Build37/BWA_INDEX_hs37d5/hs37d5.fa -V IPF0047.194173.endPosCorr.gvcf.gz -V IPF0048.194174.endPosCorr.gvcf.gz -L hs37d5 > cohort.2.2.hs37d5.txt
The ERROR message received:
CombineGVCF was succesful till hs37d5:24140804 and Failed at hs37d5:24140805. I think the error is because of a site with higher number of Alternate Indel Alleles in 1 sample --
Screen shot of hs37d5:24140805 in Sample2
Would really appreciate any help in this regard...
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