depristo 38d7733989 Now accepts any number of VCFs to evaluate. Runs the standard (now three) variant eval commands and invokes the exomeQC R script. Has some annoying assumptions about paths encoded right now. Example usage below: ... setenv DATA ~/Desktop/broadLocal/localData/ java -Djava.io.tmpdir=tmp -jar ../dist/Queue.jar -S ../scala/qscript/oneoffs/depristo/ExomePostQCEval.scala --gatkjarfile ../dist/GenomeAnalysisTK.jar -R $DATA/human_g1k_v37.fasta $* -eval $DATA/ESPGO_Gabriel_NHLBI_eomi_june_2011_batch1.vcf -intervals ~/Desktop/broadLocal/localData/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list -dbSNP ~/Desktop/broadLocal/localData/dbsnp_132_b37.vcf -eval $DATA/ESPGO_Gabriel_NHLBI_eomi_june_2011_batch2.vcf git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6004 348d0f76-0448-11de-a6fe-93d51630548a		2011-06-16 12:49:54 +00:00
..
qscript	Now accepts any number of VCFs to evaluate. Runs the standard (now three) variant eval commands and invokes the exomeQC R script. Has some annoying assumptions about paths encoded right now. Example usage below:	2011-06-16 12:49:54 +00:00
src/org/broadinstitute/sting	samtools merge requires indexed files, so added them as implicit inputs.	2011-06-08 15:02:51 +00:00
test/org/broadinstitute/sting/queue	Minor update so the debug messages don't show temp files as chromosome 208799060637697164972	2011-05-26 22:56:33 +00:00