# HG changeset patch # User jeremie # Date 1404290440 14400 # Node ID 3ce285e7c6da1c41e9ecdd1c4407883dffc8f3d0 # Parent 544c5266fc0fa373ada910d30df5528c6ea7dd00 Uploaded diff -r 544c5266fc0f -r 3ce285e7c6da pindel.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pindel.xml Wed Jul 02 04:40:40 2014 -0400 @@ -0,0 +1,153 @@ + + + + + + pindel.py + + -r $inputReferenceFile + -b $inputBamFile + -s $insertSize + -o $outputVcfFile + -n $sampleTag + + #if $breakdancer.checking == "yes": + -input1 $breakdancer.input1 + #end if + --number_of_threads $number_of_threads + --window_size $window_size + --sequencing_error_rate $sequencing_error_rate + --sensitivity $sensitivity + #if $reportInversions: + --report_inversions + #end if + #if $reportDuplications: + --report_duplications + #end if + #if $reportLongInsertions: + --report_long_insertions + #end if + #if $reportBreakpoints: + --report_breakpoints + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file