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I am working on exome capture data for barley (1.3Gbp). I am interested in variant calling to find out SNPs in my sample. I have used SAMTools SNP calling and things get done in ~1 hr whereas GATK (inspite of its several steps to prepare the BAM for variant caller) takes forever. I understand my reference is large and since its an exome capture the targeted region is only 60 Mbp of 1.3Gbp. RealignerTargetCreator is the step it takes forever to locate for sites where indel realignment is required. Do someone have any suggestions to speed it up? Or try any other variant caller? I have tried downsampling my BAM with samtools view -s and that too takes as the log says 8 more days to finish :(
Here is my sample command:
java -Xmx20g -XX:MaxPermSize=40G -jar /software/production/gatk/2.3.9/x86_64/GenomeAnalysisTK.jar -T RealignerTargetCreator -I in.bam -R ref.fa -o out.bam