# HG changeset patch
# User devteam
# Date 1429646431 14400
# Node ID 87398ae795c7b49263b856bfa79e2b9faa5ade4f
Uploaded
diff -r 000000000000 -r 87398ae795c7 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue Apr 21 16:00:31 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 $2 }'
+
+
+
+
+
+
+
+-----
+
+.. class:: warningmark
+
+**No options available? How to re-detect metadata**
+
+If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps:
+
+1. Click on the **pencil** icon adjacent to the dataset in the history
+2. A new menu will appear in the center pane of the interface
+3. Click **Datatype** tab
+4. Set **New Type** to **BAM**
+5. Click **Save**
+
+The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down.
+
+
+
+
diff -r 000000000000 -r 87398ae795c7 samtools_idxstats.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_idxstats.xml Tue Apr 21 16:00:31 2015 -0400
@@ -0,0 +1,72 @@
+
+ tabulate mapping statistics for BAM dataset
+
+ macros.xml
+
+
+
+
+ "${output}" ;
+else
+ samtools idxstats "${input}" > "${output}" ;
+fi]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+`_ for the samtools idxstats command
+]]>
+
+
+
diff -r 000000000000 -r 87398ae795c7 test-data/phiX.bam
Binary file test-data/phiX.bam has changed
diff -r 000000000000 -r 87398ae795c7 test-data/samtools_idxstats_out.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samtools_idxstats_out.tabular Tue Apr 21 16:00:31 2015 -0400
@@ -0,0 +1,2 @@
+phiX174 5386 972 18
+* 0 0 10
diff -r 000000000000 -r 87398ae795c7 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Tue Apr 21 16:00:31 2015 -0400
@@ -0,0 +1,6 @@
+
+
+
+
+
+