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Error : CalculateGenotypePosteriors in GATK


Hi all,
I utilized CalculateGenotypePosteriors (GATK-3.4) walker as a step1 in Genotype Refinement. It prompts me an error message. Note that i have trios sample of 3 individuals. I checked the VCF file at corresponding location of error at 1:1549750 site in VCF, My AC=2, MLEAC=2 and i check in sample 2 heterozygotes sample are present at that site. I did not find supporting file : "ALL.phase3.20130502.biallelic_snps.integrated.sites.vcf" in bundle. So that's why i utilized supporting files that i had utilized during VQSR.

can you please help me how i can get through this issue ?

My command arguments were:
java -Xmx10g -jar /GATK-3.4/GenomeAnalysisTK.jar -T CalculateGenotypePosteriors \
-log /GENOTYPE-REFINE1/HC/step1_posteriors.log \
-R /Ref/human_g1k_v37.fasta \
--supporting /Ref/hapmap_3.3.b37.vcf \
--supporting /Ref/1000G_omni2.5.b37.vcf \
--supporting /Ref/1000G_phase1.snps.high_confidence.b37.vcf \
--supporting /Ref/Mills_and_1000G_gold_standard.indels.b37.vcf \
-V /PROJECT/GATK/VQSR/VQSR_snp_indel_CHG000691_2_3.vcf \

ERROR MESSAGE: Variant does not contain the same number of MLE allele counts as alternate alleles for record at 1:1549750

Thank you very much!

Best Answer


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