User:Lindenb/Notebook/UMR915/20100709

CALLING WITH GATK
need to index the human genome with picard CreateSequenceDictionary java -jar /usr/local/package/picard-tools-1.22/CreateSequenceDictionary.jar R=hg18.fa O=hg18.dict

calling GATK, filtering with posfilter

for I in Brs1 Brs2 Brs3 Brs4 Brs5 Brs6 Brs7 Brs8 Brs9 Brs10 do 	echo "processing $I :" java -jar /usr/local/package/gatk/GenomeAnalysisTK-1.0.3471/GenomeAnalysisTK.jar \ -T UnifiedGenotyper -R /GENOTYPAGE/data/pubdb/ucsc/hg18/chromosomes/hg18.fa \ -pl SOLEXA -I ../20100607_mapping/recal_bwa_rmdup_${I}.bam |\ java -jar ~/src/code915/dist/posfilter.jar \ -db *_PCCR.bed -vcf |\ gzip --best > gatk_call_${I}.vcf.gz  done