We are following "Calling variants on cohorts of samples using the HaplotypeCaller in GVCF mode" best practices using GATK 3.8.1 and Java 1.8. Thus we merged the raw.g.vcfs from HaplotypeCaller into one cohort.g.vcf and then carried out joint genotyping using the GenotypeGVCFs tool. We are working in a haploid model organism so we then tried to use the VariantFiltration tool on the output (which is a vcf file containing the information from all of the sequences with which we are working). However this failed and we got the error
"Line 2176: there aren't enough columns for line 102"
Others have encountered the same problem and I see that you have responded that the GATK and java versions are incompatible but this was several versions ago. Is this true for us? Please can you tell me where to go to next.
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GenotypeGVCFs and VariantFiltration tools
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