# HG changeset patch # User devteam # Date 1429646213 14400 # Node ID 0072bf5937917a552e825b265f69ea7dac50fd0b # Parent a3dd61e7bec174240a772f8141041e23b73a610d Uploaded diff -r a3dd61e7bec1 -r 0072bf593791 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Apr 21 15:56:53 2015 -0400 @@ -0,0 +1,70 @@ + + + + samtools + + + + + + + @misc{SAM_def, + title={Definition of SAM/BAM format}, + url = {https://samtools.github.io/hts-specs/SAMv1.pdf},} + + 10.1093/bioinformatics/btp352 + 10.1093/bioinformatics/btr076 + 10.1093/bioinformatics/btr509 + + @misc{Danecek_et_al, + Author={Danecek, P., Schiffels, S., Durbin, R.}, + title={Multiallelic calling model in bcftools (-m)}, + url = {http://samtools.github.io/bcftools/call-m.pdf},} + + + @misc{Durbin_VCQC, + Author={Durbin, R.}, + title={Segregation based metric for variant call QC}, + url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} + + + @misc{Li_SamMath, + Author={Li, H.}, + title={Mathematical Notes on SAMtools Algorithms}, + url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} + + + @misc{SamTools_github, + title={SAMTools GitHub page}, + url = {https://github.com/samtools/samtools},} + + + + + samtools --version | head -n 1 | awk '{ print $2 }' + + + + + + + +----- + +.. class:: warningmark + +**No options available? How to re-detect metadata** + +If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps: + +1. Click on the **pencil** icon adjacent to the dataset in the history +2. A new menu will appear in the center pane of the interface +3. Click **Datatype** tab +4. Set **New Type** to **BAM** +5. Click **Save** + +The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down. + + + + diff -r a3dd61e7bec1 -r 0072bf593791 samtools_flagstat.xml --- a/samtools_flagstat.xml Thu Mar 27 15:23:45 2014 -0400 +++ b/samtools_flagstat.xml Tue Apr 21 15:56:53 2015 -0400 @@ -1,8 +1,11 @@ - - - samtools - - provides simple stats on BAM files + + tabulate descriptive stats for BAM datset + + macros.xml + + + + samtools flagstat "$input1" > "$output1" @@ -13,7 +16,7 @@ - + @@ -21,17 +24,22 @@ **What it does** -This tool uses the SAMTools_ toolkit to produce simple stats on a BAM file. - -.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml - ------- +Uses ``samtools flagstat`` command to print descriptive information for a BAM dataset. Here is an example of such information:: -**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.* - + 200 + 0 in total (QC-passed reads + QC-failed reads) + 0 + 0 secondary + 0 + 0 supplementary + 0 + 0 duplicates + 25 + 0 mapped (12.50%:nan%) + 200 + 0 paired in sequencing + 100 + 0 read1 + 100 + 0 read2 + 0 + 0 properly paired (0.00%:nan%) + 0 + 0 with itself and mate mapped + 25 + 0 singletons (12.50%:nan%) + 0 + 0 with mate mapped to a different chr + 0 + 0 with mate mapped to a different chr (mapQ>=5) + + diff -r a3dd61e7bec1 -r 0072bf593791 test-data/3unsorted.bam Binary file test-data/3unsorted.bam has changed diff -r a3dd61e7bec1 -r 0072bf593791 test-data/samtools_flagstat_input1.bam Binary file test-data/samtools_flagstat_input1.bam has changed diff -r a3dd61e7bec1 -r 0072bf593791 test-data/samtools_flagstat_out1.txt --- a/test-data/samtools_flagstat_out1.txt Thu Mar 27 15:23:45 2014 -0400 +++ b/test-data/samtools_flagstat_out1.txt Tue Apr 21 15:56:53 2015 -0400 @@ -1,11 +1,13 @@ -10 + 0 in total (QC-passed reads + QC-failed reads) +200 + 0 in total (QC-passed reads + QC-failed reads) +0 + 0 secondary +0 + 0 supplementary 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%) +25 + 0 mapped (12.50%:nan%) +200 + 0 paired in sequencing +100 + 0 read1 +100 + 0 read2 +0 + 0 properly paired (0.00%:nan%) 0 + 0 with itself and mate mapped -0 + 0 singletons (nan%:nan%) +25 + 0 singletons (12.50%:nan%) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5) diff -r a3dd61e7bec1 -r 0072bf593791 tool_dependencies.xml --- a/tool_dependencies.xml Thu Mar 27 15:23:45 2014 -0400 +++ b/tool_dependencies.xml Tue Apr 21 15:56:53 2015 -0400 @@ -1,6 +1,6 @@ - - + +