# HG changeset patch
# User brenninc
# Date 1462867157 14400
# Node ID 97bb72be07f97dec38ee3bf80b1006f3ab1fe94f
Uploaded first version
diff -r 000000000000 -r 97bb72be07f9 samtools_flag_filter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_flag_filter.xml Tue May 10 03:59:17 2016 -0400
@@ -0,0 +1,104 @@
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+ Use Samtools' view tool to filter alignments based on the flag field.
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+ samtools_macros.xml
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diff -r 000000000000 -r 97bb72be07f9 samtools_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_macros.xml Tue May 10 03:59:17 2016 -0400
@@ -0,0 +1,72 @@
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+ samtools
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+ @misc{SAM_def,
+ title={Definition of SAM/BAM format},
+ url = {https://samtools.github.io/hts-specs/SAMv1.pdf},}
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+ 10.1093/bioinformatics/btp352
+ 10.1093/bioinformatics/btr076
+ 10.1093/bioinformatics/btr509
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+ @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},}
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+ @misc{Durbin_VCQC,
+ Author={Durbin, R.},
+ title={Segregation based metric for variant call QC},
+ url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
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+ @misc{Li_SamMath,
+ Author={Li, H.},
+ title={Mathematical Notes on SAMtools Algorithms},
+ url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
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+ @misc{SamTools_github,
+ title={SAMTools GitHub page},
+ url = {https://github.com/samtools/samtools},}
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+ samtools --version | head -n 1 | awk '{ print $2 }'
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+-----
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+.. class:: warningmark
+
+**No options available? How to re-detect metadata**
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+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:
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+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**
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+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.
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diff -r 000000000000 -r 97bb72be07f9 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Tue May 10 03:59:17 2016 -0400
@@ -0,0 +1,6 @@
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