# HG changeset patch
# User devteam
# Date 1377541457 14400
# Node ID 7e92b2a53aab8cf84e024fe45901cb9920f9e08a
Uploaded
diff -r 000000000000 -r 7e92b2a53aab samtools_rmdup.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_rmdup.xml Mon Aug 26 14:24:17 2013 -0400
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+ samtools
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+ remove PCR duplicates
+ samtools rmdup
+ #if str( $bam_paired_end_type.bam_paired_end_type_selector ) == "PE"
+ ${bam_paired_end_type.force_se}
+ #else:
+ -s
+ #end if
+ "$input1" "$output1"
+ 2>&1 || echo "Error running samtools rmdup." >&2
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+**What it does**
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+This tool uses the SAMTools_ toolkit to remove potential PCR duplicates: if multiple read pairs have identical external coordinates, only retain the pair with highest mapping quality. In the paired-end mode, this command ONLY works with FR orientation and requires ISIZE is correctly set. It does not work for unpaired reads (e.g. two ends mapped to different chromosomes or orphan reads).
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+.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
+
+------
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+**Citation**
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+For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_
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+If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
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diff -r 000000000000 -r 7e92b2a53aab test-data/1.bam
Binary file test-data/1.bam has changed
diff -r 000000000000 -r 7e92b2a53aab tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Mon Aug 26 14:24:17 2013 -0400
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