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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