# HG changeset patch # User devteam # Date 1377016424 14400 # Node ID 1bbde47ebd2a956f94b3d88da4b285eb13d39973 Uploaded diff -r 000000000000 -r 1bbde47ebd2a samtools_flagstat.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools_flagstat.xml Tue Aug 20 12:33:44 2013 -0400 @@ -0,0 +1,37 @@ + + + samtools + + provides simple stats on BAM files + samtools flagstat "$input1" > "$output1" + + + + + + + + + + + + + + + +**What it does** + +This tool uses the SAMTools_ toolkit to produce simple stats on a BAM file. + +.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml + +------ + +**Citation** + +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>`_ + +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + + + diff -r 000000000000 -r 1bbde47ebd2a test-data/3unsorted.bam Binary file test-data/3unsorted.bam has changed diff -r 000000000000 -r 1bbde47ebd2a test-data/samtools_flagstat_out1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_flagstat_out1.txt Tue Aug 20 12:33:44 2013 -0400 @@ -0,0 +1,11 @@ +10 + 0 in total (QC-passed reads + QC-failed reads) +0 + 0 duplicates +10 + 0 mapped (100.00%:nan%) +0 + 0 paired in sequencing +0 + 0 read1 +0 + 0 read2 +0 + 0 properly paired (nan%:nan%) +0 + 0 with itself and mate mapped +0 + 0 singletons (nan%:nan%) +0 + 0 with mate mapped to a different chr +0 + 0 with mate mapped to a different chr (mapQ>=5) diff -r 000000000000 -r 1bbde47ebd2a tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Aug 20 12:33:44 2013 -0400 @@ -0,0 +1,6 @@ + + + + + +