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setting value for parameter ploidy

anand_mtanand_mt Posts: 3Member


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" -I $basename"_B.realigned.bam" -I $basename"_C.realigned.bam" -I $basename"_D.realigned.bam" -ploidy 4 -o $basename.snps.vcf -stand_call_conf 25.0 -stand_emit_conf 10.0

Thank you.

Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,530Administrator, GATK Developer admin

    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

  • anand_mtanand_mt Posts: 3Member


    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..

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