Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
changeset 65:19360b35f760 draft
Uploaded
author | yhoogstrate |
---|---|
date | Wed, 05 Mar 2014 11:08:26 -0500 |
parents | bafa6c859303 |
children | ef13be78c5fc |
files | varscan_mpileup2snp_from_bam.xml |
diffstat | 1 files changed, 4 insertions(+), 5 deletions(-) [+] |
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--- a/varscan_mpileup2snp_from_bam.xml Wed Mar 05 11:08:17 2014 -0500 +++ b/varscan_mpileup2snp_from_bam.xml Wed Mar 05 11:08:26 2014 -0500 @@ -65,7 +65,7 @@ #for $alignment in $alignments ${alignment} #end for - 2> stderr_1.txt + 2>stderr_1.txt #if $sort_mpileup | sort -k 1,1 -k 2,2 @@ -83,16 +83,15 @@ --min-var-freq $varscan_min_var_freq --min-freq-for-hom $varscan_min_freq_for_hom --p-value $varscan_p_value - $varscan_strand_filter - $varscan_output_vcf - $varscan_variants + $varscan_strand_filter + $varscan_variants #end if #if $varscan_output_vcf --output-vcf 1 #end if - 2> stderr_2.txt + 2>stderr_2.txt > $snv_output ; echo "-------------------------[ mpileup generation ]-------------------------" ;