Mercurial > repos > stef > falco
changeset 36:6c8ef3d7584e draft
Uploaded
author | stef |
---|---|
date | Fri, 10 Oct 2014 10:49:16 -0400 |
parents | 8bc2e1a67449 |
children | eb9a8e3a3682 |
files | falco/amplicon-VcAn-TSACP.sh |
diffstat | 1 files changed, 38 insertions(+), 38 deletions(-) [+] |
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--- a/falco/amplicon-VcAn-TSACP.sh Fri Oct 10 10:45:56 2014 -0400 +++ b/falco/amplicon-VcAn-TSACP.sh Fri Oct 10 10:49:16 2014 -0400 @@ -26,26 +26,26 @@ fi # Annotation -VcfIn=$output.vcf -VcfOut=$output.samtools.vcf +#VcfIn=$output.vcf +#VcfOut=$output.samtools.vcf -if [ ! -e $VcfOut ] -then +#if [ ! -e $VcfOut ] +#then # Samtools annotation -echo `date` " [$$] - $java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > tmp.snpeff.vcf" -$java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > $output.snpeff.vcf -echo `date` " [$$] - Done!" +#echo `date` " [$$] - $java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > tmp.snpeff.vcf" +#$java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > $output.snpeff.vcf +#echo `date` " [$$] - Done!" -echo `date` " [$$] - $java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf" -$java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf -mv $output.snpeff.2.vcf $VcfOut -echo `date` " [$$] - Done!" +#echo `date` " [$$] - $java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf" +#$java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf +#mv $output.snpeff.2.vcf $VcfOut +#echo `date` " [$$] - Done!" -echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf" +#echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf" #$java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf #mv $output.snpeff.3.vcf $VcfOut -echo `date` " [$$] - Done!" -fi +#echo `date` " [$$] - Done!" +#fi if [ ! -e $output.qc.ann.txt ] then @@ -75,46 +75,46 @@ -VcfIn=$output.qc.ann.filt.vcf -VcfOut=$output.qc.ann.filt.a.vcf +#VcfIn=$output.qc.ann.filt.vcf +#VcfOut=$output.qc.ann.filt.a.vcf -if [ ! -e $VcfOut ] -then +#if [ ! -e $VcfOut ] +#then # qc vcf annotation -echo `date` " [$$] - $java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > tmp.snpeff.vcf" -$java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > $output.snpeff.vcf -echo `date` " [$$] - Done!" +#echo `date` " [$$] - $java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > tmp.snpeff.vcf" +#$java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > $output.snpeff.vcf +#echo `date` " [$$] - Done!" -echo `date` " [$$] - $java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf" -$java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf -mv $output.snpeff.2.vcf $VcfOut -echo `date` " [$$] - Done!" +#echo `date` " [$$] - $java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf" +#$java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf +#mv $output.snpeff.2.vcf $VcfOut +#echo `date` " [$$] - Done!" #echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf" #$java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf #mv $output.snpeff.3.vcf $VcfOut #echo `date` " [$$] - Done!" -fi +#fi -VcfIn=$output.qc.ann.clinvar.vcf -VcfOut=$output.qc.ann.clinvar.a.vcf +#VcfIn=$output.qc.ann.clinvar.vcf +# VcfOut=$output.qc.ann.clinvar.a.vcf -if [ ! -e $VcfOut ] -then +#if [ ! -e $VcfOut ] +#then # qc vcf annotation -echo `date` " [$$] - $java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > tmp.snpeff.vcf" -$java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > $output.snpeff.vcf -echo `date` " [$$] - Done!" +#echo `date` " [$$] - $java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > tmp.snpeff.vcf" +#$java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > $output.snpeff.vcf +#echo `date` " [$$] - Done!" -echo `date` " [$$] - $java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf" -$java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf -mv $output.snpeff.2.vcf $VcfOut -echo `date` " [$$] - Done!" +#echo `date` " [$$] - $java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf" +#$java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf +#mv $output.snpeff.2.vcf $VcfOut +#echo `date` " [$$] - Done!" #echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf" #$java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf #mv $output.snpeff.3.vcf $VcfOut #echo `date` " [$$] - Done!" -fi +#fi