Post date: Nov 02, 2015 3:9:20 AM
We designated diploids and triploids based on our calculations from the LDA (here is the file). In particular, we called triploids or diploids if the probability of being a triploid or diploid was greater than 0.75. We called 113 diploids and 54 triploids using these criteria; in most cases our call matched previous data (104 match 8 missmatch for dips; 43 match and 10 missmatch for trips). I created bam file lists for these individuals and used GATK's UnifiedGenotyper for variant calling. The specific commands are below.
java -jar -Xmx236g -Djava.io.tmpdir=/pscratch/A01963476/ /rc/tools/free/redhat_6_x86_64/gatk-3.1.1/GenomeAnalysisTK.jar -T UnifiedGenotyper -R /labs/evolution/data/aspen/genome/Potrs01-genome.fa -I mydipbam.list -o aspenvariantsDIP.vcf -nt 32 -glm SNP -hets 0.001 -mbq 20 -ploidy 2 -stand_call_conf 50 -maxAltAlleles 2
java -jar -Xmx236g -Djava.io.tmpdir=/pscratch/A01963476/ /rc/tools/free/redhat_6_x86_64/gatk-3.1.1/GenomeAnalysisTK.jar -T UnifiedGenotyper -R /labs/evolution/data/aspen/genome/Potrs01-genome.fa -I mytripbam.list -o aspenvariantsTRIP.vcf -nt 22 -glm SNP -hets 0.001 -mbq 20 -ploidy 3 -stand_call_conf 50 -maxAltAlleles 2