The current GATK version is 3.2-2

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# setting value for parameter ploidy

Posts: 3Member

Hi,

Just wanted to confirm.. I have a data from 4 spores of a yeast (haploid) tetrad.. If I want to call out variants using all 4 spores (4 bam files), do I need to set -ploidy as 1 or as 4 (Number of samples in each pool * Sample Ploidy) ??

This is the code I am using:

java -d64 -Xms1g -Xmx4g -jar GenomeAnalysisTK.jar -glm SNP -nt 52 -R genome.fasta -T UnifiedGenotyper -I basename"_A.realigned.bam" -Ibasename"_B.realigned.bam" -I basename"_C.realigned.bam" -Ibasename"_D.realigned.bam" -ploidy 4 -o \$basename.snps.vcf -stand_call_conf 25.0 -stand_emit_conf 10.0


Thank you.

Tagged:

If each spore is identified as a separate haploid sample, then ploidy should be 1. The pooled ploidy formulat is only for a specific type of sample pooling.

Geraldine Van der Auwera, PhD

• Posts: 3Member

Hi,

Thank you for the answer. Each spore is considered haploid .. and do I need to set -pnrm EXACT_INDEPENDENT ?? Sorry this is my first time using GATK.. I am bit confused with the parameters..