Post date: May 13, 2015 6:47:39 PM
The alfalfa genome was prepared for variant calling with GATK (dictionary and index files):
java -jar /labs/evolution/Source/picard-tools-1.115/CreateSequenceDictionary.jar R=final.assembly.fasta O=final.assembly.dict
samtools faidx final.assembly.fasta
Then, GATK was used for variant calling with ploidy set to 4:
java -jar -Xmx92g -Djava.io.tmpdir=/pscratch/A01963476/ /rc/tools/free/redhat_6_x86_64/gatk-3.1.1/GenomeAnalysisTK.jar -T UnifiedGenotyper -R /pscratch/A01963476/data/gbsGomp006to008/Alignments/final.assembly.fasta -I bams.list -o alfalfavariants.vcf -nt 8 -glm SNP -hets 0.001 -mbq 20 -ploidy 4 -stand_call_conf 50 -maxAltAlleles 2
Note, I am trying a virtual machine with 92 gigs of memory to see whether or not this is enough for this smaller data set.