I was trying to do combine sets of vcf files for all my samples so that I have one single vcf output using this command option below
java -d64 -Xmx48g -jar ${GATK}/GenomeAnalysisTK.jar \
-R ${REF} \
-T GenotypeGVCFs \
--variant A.g.vcf \
--variant B.g.vcf \
--variant C.g.vcf \
-stand_emit_conf 30 \
-stand_call_conf 30 \
-o genotype.vcf
but I got this error message
“The following invalid GT allele index was encountered in the file: END=21994810”. I have tried to locate where the problem could be coming from but I do not understand this. Could you please advise me.