User:Lindenb/Notebook/UMR915/20100709

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20100708        Top        20100712       


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
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