Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
changeset 82:bf44ae0d9264 draft
Uploaded
author | yhoogstrate |
---|---|
date | Thu, 12 Jun 2014 08:25:53 -0400 |
parents | 404583a3d754 |
children | 23ed370b8d98 |
files | test-data/GSM1244820_Control_Rep5.hg18.subset.bam tool_dependencies.xml varscan_mpileup2snp.xml varscan_mpileup2snp_from_bam.xml |
diffstat | 4 files changed, 26 insertions(+), 32 deletions(-) [+] |
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--- a/tool_dependencies.xml Wed Jun 11 05:57:04 2014 -0400 +++ b/tool_dependencies.xml Thu Jun 12 08:25:53 2014 -0400 @@ -1,9 +1,11 @@ <?xml version="1.0"?> <tool_dependency> + <!-- <package name="ncurses" version="5.9"> <repository changeset_revision="f62fa47b852d" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> + --> <package name="samtools_parallel_mpileup_0_1_19a" version="0.1.19a"> <install version="1.0"> @@ -40,12 +42,6 @@ </readme> </package> - <!-- - <package name="package_samtools_0_1_19" version="0.1.19"> - <repository changeset_revision="40250a414486" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> - </package> - --> - <package name="ncurses" version="5.9"> <repository changeset_revision="40250a414486" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package>
--- a/varscan_mpileup2snp.xml Wed Jun 11 05:57:04 2014 -0400 +++ b/varscan_mpileup2snp.xml Thu Jun 12 08:25:53 2014 -0400 @@ -6,19 +6,19 @@ </requirements> <command> cat $mpileup_input | java - -Xmx64G - -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar - mpileup2snp + -Xmx64G + -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar + mpileup2snp #if $extended_parameters.parameters == "extended" - --min-coverage $varscan_min_coverage - --min-reads2 $varscan_min_reads2 - --min-avg-qual $varscan_min_avg_qual - --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_variants + --min-coverage $extended_parameters.varscan_min_coverage + --min-reads2 $extended_parameters.varscan_min_reads2 + --min-avg-qual $extended_parameters.varscan_min_avg_qual + --min-var-freq $extended_parameters.varscan_min_var_freq + --min-freq-for-hom $extended_parameters.varscan_min_freq_for_hom + --p-value $extended_parameters.varscan_p_value + $extended_parameters.varscan_strand_filter + $extended_parameters.varscan_variants #end if #if $varscan_output == "vcf" or $varscan_output.value == "vcf"
--- a/varscan_mpileup2snp_from_bam.xml Wed Jun 11 05:57:04 2014 -0400 +++ b/varscan_mpileup2snp_from_bam.xml Thu Jun 12 08:25:53 2014 -0400 @@ -14,6 +14,7 @@ #else #import os.path #for $alignment in $alignments + <!-- @todo use the existence of $alignment.metadata.bam_index or $alignment.metadata['bam_index'] --> #if not os.path.isfile(str($alignment)+".bai") echo "- Indexing alignment file: $alignment.name " ; samtools index $alignment 2>&1 ; @@ -91,14 +92,14 @@ mpileup2snp #if $extended_parameters.parameters == "extended" - --min-coverage $varscan_min_coverage - --min-reads2 $varscan_min_reads2 - --min-avg-qual $varscan_min_avg_qual - --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_variants + --min-coverage $extended_parameters.varscan_min_coverage + --min-reads2 $extended_parameters.varscan_min_reads2 + --min-avg-qual $extended_parameters.varscan_min_avg_qual + --min-var-freq $extended_parameters.varscan_min_var_freq + --min-freq-for-hom $extended_parameters.varscan_min_freq_for_hom + --p-value $extended_parameters.varscan_p_value + $extended_parameters.varscan_strand_filter + $extended_parameters.varscan_variants #end if #if $varscan_output == "vcf" or $varscan_output.value == "vcf" @@ -108,17 +109,14 @@ 2>stderr_2.txt > $snv_output ; - echo "-------------------------[ mpileup generation ]-------------------------" ; - echo "" ; + + echo "---------------[ mpileup generation ]---------------" ; cat stderr_1.txt ; echo "" ; - echo "" ; - echo "-------------------------[ VarScan SNP detect ]-------------------------" ; - echo "" ; - echo "" ; + echo "---------------[ VarScan SNP detect ]---------------" ; cat stderr_2.txt ; echo "" ; - echo "------------------------------------------------------------------------" ; + echo "----------------------------------------------------" ; #end if </command>