Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
changeset 57:83d480908f4b draft
Uploaded
author | yhoogstrate |
---|---|
date | Wed, 05 Mar 2014 09:49:46 -0500 |
parents | 62219bff4fbf |
children | 5109a0f2cb25 |
files | varscan_mpileup2snp_from_bam.xml |
diffstat | 1 files changed, 13 insertions(+), 19 deletions(-) [+] |
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--- a/varscan_mpileup2snp_from_bam.xml Wed Mar 05 09:49:39 2014 -0500 +++ b/varscan_mpileup2snp_from_bam.xml Wed Mar 05 09:49:46 2014 -0500 @@ -84,10 +84,13 @@ #end if --output-vcf $varscan_output_vcf + 2> stderr_2.txt - #if $sort_mpileup == "true" + + #if $sort_mpileup | sort -k 1,1 -k 2,2 #end if + > $snv_output ; echo "-------------------------[ mpileup generation ]-------------------------" ; @@ -227,17 +230,13 @@ <tests> <test><!-- Use classical samtools --> <param name="alignments" value="hg19_mutant.bam.txt" dbkey="hg19" ftype="bam" /> - <!-- <param name="reference_genome_source.source_select" value="attribute" /> --> - <param name="source_select" value="attribute" /> - <!-- <param name="extended_parameters_regions.samtools_regions" value="entire_genome" /> --> - <param name="samtools_regions" value="entire_genome" /> + <param name="source_select" value="attribute" /> + <param name="samtools_regions" value="entire_genome" /> - <!-- <param name="mpileup_parallelization.mpileup_parallelization_select" value="false" /> --> - <param name="mpileup_parallelization_select" value="false" /> + <param name="mpileup_parallelization_select" value="false" /> <param name="sort_mpileup" value="true" /> - <!-- <param name="extended_parameters.parameters" value="default" /> --> - <param name="parameters" value="default" /> + <param name="parameters" value="default" /> <param name="varscan_output_vcf" value="1" /> @@ -245,19 +244,14 @@ </test> <test><!-- Use parallelized samtools --> <param name="alignments" value="hg19_mutant.bam.txt" dbkey="hg19" ftype="bam" /> - <!-- <param name="reference_genome_source.source_select" value="attribute" /> --> - <param name="source_select" value="attribute" /> - <!-- <param name="extended_parameters_regions.samtools_regions" value="entire_genome" /> --> - <param name="samtools_regions" value="entire_genome" /> + <param name="source_select" value="attribute" /> + <param name="samtools_regions" value="entire_genome" /> - <!-- <param name="mpileup_parallelization.mpileup_parallelization_select" value="true" /> --> - <param name="mpileup_parallelization_select" value="true" /> - <!-- <param name="mpileup_parallelization.samtools_threads" value="2" /> --> - <param name="samtools_threads" value="2" /> + <param name="mpileup_parallelization_select" value="true" /> + <param name="samtools_threads" value="2" /> <param name="sort_mpileup" value="true" /> - <!-- <param name="extended_parameters.parameters" value="default" /> --> - <param name="parameters" value="default" /> + <param name="parameters" value="default" /> <param name="varscan_output_vcf" value="1" />