SnpEff

= Annotation snpEff = snpEff="/ngs1a/01-script/snpeff/snpEff_2_0_5" java -Xmx${heap}m \ -jar  ${snpEff}/snpEff.jar  \ eff  \ -v -i vcf \ -o vcf  \ -c   ${snpEff}/snpEff.config GRCh37.65  \ $PWDS/variants/${subjectID}.snps.PASS.vcf java -Xmx${heap}m \ -jar  ${snpEff}/snpEff.jar  \ eff  \ -v -i vcf \ -o vcf  \ -c   ${snpEff}/snpEff.config GRCh37.65  \ $PWDS/variants/${subjectID}.indels.PASS.vcf Example: for subjectID in B1001    B117001  B130008  B22001   B263001  B3001    B33001   B407001  B415001  B425001  B437001  B447001  B457001  B75001    BP200001  C10  C17  C23  C30  C37  C44  C51  C8 B102001  B118001  B13001   B233001  B264001  B301001  B35001   B408001  B417001  B426001  B439001  B448001  B57004   B79001    BP210001  C11  C18  C24  C31  C38  C45  C52  C9  B103013  B119001  B132001  B240001  B266001  B302002  B39001   B409001  B418001  B428001  B440001  B45001   B58001   B84001    BP242001  C12  C19  C25  C32  C39  C46  C53  B106001  B12001   B202001  B24001   B267001  B303001  B4001    B410001  B419001  B430001  B442001  B451001  B61001   B86001    BP252006  C13  C2   C26  C33  C40  C47  C54  B111001  B122001  B203001  B251001  B27001   B304001  B402005  B411001  B420001  B431001  B443006  B452001  B62001   B9001     BP257001  C14  C20  C27  C34  C41  C48  C55  B113001  B124001  B204001  B256001  B300001  B308001  B403001  B412001  B421001  B432001  B444008  B455001  B63001   BP112001  BP65001   C15  C21  C28  C35  C42  C49  C56  B115001  B128001  B217001  B261005  B30001   B31001   B404001  B414001  B424001  B435001  B446001  B456001  B64001   BP131004  BP99001   C16  C22  C29  C36  C43  C50  C7

do

PWDS="/ngs1a/04-synaptome-year1/01-Done/${subjectID}/analysis/" heap=4000 snpEff="/ngs1a/01-script/snpeff/snpEff_2_0_5" mkdir $PWDS/variants-gatk/snpEff cd $PWDS/variants-gatk/snpEff

java -Xmx${heap}m \ -jar  ${snpEff}/snpEff.jar  \ eff  \ -v -i vcf \ -o vcf  \ -s $PWDS/variants-gatk/snpEff/${subjectID}.snps.PASS.snpEff.summary.html \ -c   ${snpEff}/snpEff.config  \ GRCh37.65  \ $PWDS/variants-gatk/${subjectID}.snps.PASS.vcf  \ > $PWDS/variants-gatk/snpEff/${subjectID}.snps.PASS.snpEff.annotate.vcf java -Xmx${heap}m \ -jar  ${snpEff}/snpEff.jar  \ eff  \ -v -i vcf \ -o vcf  \ -s $PWDS/variants-gatk/snpEff/${subjectID}.indels.PASS.snpEff.summary.html \ -c   ${snpEff}/snpEff.config  \ GRCh37.65  \ $PWDS/variants-gatk/${subjectID}.indels.PASS.vcf  \ > $PWDS/variants-gatk/snpEff/${subjectID}.indels.PASS.snpEff.annotate.vcf done

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