Test-drive the GATK tools and Best Practices pipelines on Terra
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ploidy level in UnifiedGenotyper
We have a pooling of 64 samples and the organism is diploid, we are using ploidy of 128 (64x2=128). Whether we can use such a high ploidy with UnifiedGenotyper. The command line which we have used is below
java -jar -Xmx8g /home/prateek/Downloads/GenomeAnalysisTK.jar -T UnifiedGenotyper -R tilling.fa -I d12_S44.sorted.bam -o d12_S44.vcf -stand_call_conf 30.0 -stand_emit_conf 10.0 -glm BOTH -ploidy 128
whether we are using right command or what is the other alternative we can use.
What is maximum ploidy or pooling level we can use with UnifiedGenotyper.
Thanks in advance..