Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
changeset 60:cb0f5c219244 draft
Uploaded
| author | yhoogstrate |
|---|---|
| date | Wed, 05 Mar 2014 10:10:54 -0500 |
| parents | d29384007de7 |
| children | 0bab34a58764 |
| files | varscan_mpileup2snp_from_bam.xml |
| diffstat | 1 files changed, 10 insertions(+), 6 deletions(-) [+] |
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--- a/varscan_mpileup2snp_from_bam.xml Wed Mar 05 10:10:45 2014 -0500 +++ b/varscan_mpileup2snp_from_bam.xml Wed Mar 05 10:10:54 2014 -0500 @@ -66,6 +66,11 @@ ${alignment} #end for 2> stderr_1.txt + + #if $sort_mpileup + | sort -k 1,1 -k 2,2 + #end if + | java -Xmx64G -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar @@ -83,14 +88,13 @@ $varscan_variants #end if - --output-vcf $varscan_output_vcf + #if $varscan_output_vcf + --output-vcf 0 + #else + --output-vcf 0 + #end if 2> stderr_2.txt - - #if $sort_mpileup - | sort -k 1,1 -k 2,2 - #end if - > $snv_output ; echo "-------------------------[ mpileup generation ]-------------------------" ;