Hi,
I have a number of samples that consist of multiple individuals from the same population pooled together, and have been truing to use HaplotypeCaller to call the variants. I have set the (ploidy to 2 * number of individuals) but keep getting the same or similar error message, after running for several hours or days:
ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.3-0-g37228af):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: the combination of ploidy (180) and number of alleles (9) results in a very large number of genotypes (> 2147483647). You need to limit ploidy or the number of alternative alleles to analyze this locus
ERROR ------------------------------------------------------------------------------------------
and I'm not sure what I can do to rectify it... Obviously I can't limit the ploidy, it is what it is, and I thought that HC only allows a maximum of six alleles anyway?
My code is below, and any help would be appreciated.
java -Xmx24g -jar ~/bin/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar -T HaplotypeCaller
-nct 6 \
-R ~/my_ref_sequence \
--intervals ~/my_intervals_file \
-ploidy 180 \
-log my_log_file \
-I ~/my_input_bam \
-o ~/my_output_vcf