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Combination of ploidy and number of alleles ERROR when running GenotypeGVCFs

FerFer AustriaMember

Hello. I've run Haplotype caller for 19 samples in -ploidy 19 (19 is as high as I can get without getting an error for that, but that is a discussion opened elsewhere). Then, I've tried GenotypeGVCFs and get an ERROR (both command and ERROR below).

Just to add, I've run both HaplotypeCaller and GenotypeGVCFs with and without -maxAltAlleles 4 to try to limit the referred combination; however, the output is exactly the same ERROR message at the end of GenotypeGVCFs. Do you think there might be a bug or am I doing something wrong?

java -Djava.io.tmpdir=$mytmp -Xmx28g -jar GenomeAnalysisTK.jar -R $ref -T GenotypeGVCFs -o $gVCF.ploidy.vcf -V ploidy.list -ploidy 19 -maxAltAlleles 4

ERROR MESSAGE: the combination of ploidy (19) and number of alleles (21) results in a very large number of genotypes (> 2147483647). You need to limit ploidy or the number of alternative alleles to analyz
e this locus

Issue · Github
by Geraldine_VdAuwera

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