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Ploidy level in HaplotypeCaller in GATK 4.0
Thanks for the new version of GATK (GATK4.0).
We have a pooling of 48 samples and the organism is diploid, we are using ploidy of 96 (48x2=96). earlier when I am using HaplotypeCaller for variant calling in older versions of GATK, I am getting the error not enough memory to run this program., so was unable to run this with HaplotypeCaller earlier. Now when I tried it with GATK 4.0 version I am not getting this error, but a warn message mentioned below
12:40:23.159 WARN HaplotypeCallerGenotypingEngine - Removed alt alleles where ploidy is 96 and original allele count is 3, whereas after trimming the allele count becomes 2. Alleles kept are:[T*, C]
The command line which we have used is below
java -jar -Xmx64g gatk-package-188.8.131.52-local.jar HaplotypeCaller -R tilling.fa -I C1_S1.sorted.bam -O C1_S1.vcf -stand-call-conf 20.0 -ploidy 96
Can you please help us what does the warn message means, whether the command and the options which I am using are right, or I need to include more options for efficient variant calling.
Thanks in advance.