|
2
|
1 <macros>
|
|
|
2 <xml name="requirements">
|
|
|
3 <requirements>
|
|
|
4 <requirement type="package" version="1.2">samtools</requirement>
|
|
|
5 <yield/>
|
|
|
6 </requirements>
|
|
|
7 </xml>
|
|
|
8 <xml name="citations">
|
|
|
9 <citations>
|
|
|
10 <citation type="bibtex">
|
|
|
11 @misc{SAM_def,
|
|
|
12 title={Definition of SAM/BAM format},
|
|
|
13 url = {https://samtools.github.io/hts-specs/SAMv1.pdf},}
|
|
|
14 </citation>
|
|
|
15 <citation type="doi">10.1093/bioinformatics/btp352</citation>
|
|
|
16 <citation type="doi">10.1093/bioinformatics/btr076</citation>
|
|
|
17 <citation type="doi">10.1093/bioinformatics/btr509</citation>
|
|
|
18 <citation type="bibtex">
|
|
|
19 @misc{Danecek_et_al,
|
|
|
20 Author={Danecek, P., Schiffels, S., Durbin, R.},
|
|
|
21 title={Multiallelic calling model in bcftools (-m)},
|
|
|
22 url = {http://samtools.github.io/bcftools/call-m.pdf},}
|
|
|
23 </citation>
|
|
|
24 <citation type="bibtex">
|
|
|
25 @misc{Durbin_VCQC,
|
|
|
26 Author={Durbin, R.},
|
|
|
27 title={Segregation based metric for variant call QC},
|
|
|
28 url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
|
|
|
29 </citation>
|
|
|
30 <citation type="bibtex">
|
|
|
31 @misc{Li_SamMath,
|
|
|
32 Author={Li, H.},
|
|
|
33 title={Mathematical Notes on SAMtools Algorithms},
|
|
|
34 url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
|
|
|
35 </citation>
|
|
|
36 <citation type="bibtex">
|
|
|
37 @misc{SamTools_github,
|
|
|
38 title={SAMTools GitHub page},
|
|
|
39 url = {https://github.com/samtools/samtools},}
|
|
|
40 </citation>
|
|
|
41 </citations>
|
|
|
42 </xml>
|
|
|
43 <xml name="version_command">
|
|
|
44 <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
|
|
|
45 </xml>
|
|
|
46 <xml name="stdio">
|
|
|
47 <stdio>
|
|
|
48 <exit_code range="1:" level="fatal" description="Error" />
|
|
|
49 </stdio>
|
|
|
50 </xml>
|
|
|
51 <token name="@no-chrom-options@">
|
|
|
52 -----
|
|
|
53
|
|
|
54 .. class:: warningmark
|
|
|
55
|
|
|
56 **No options available? How to re-detect metadata**
|
|
|
57
|
|
|
58 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:
|
|
|
59
|
|
|
60 1. Click on the **pencil** icon adjacent to the dataset in the history
|
|
|
61 2. A new menu will appear in the center pane of the interface
|
|
|
62 3. Click **Datatype** tab
|
|
|
63 4. Set **New Type** to **BAM**
|
|
|
64 5. Click **Save**
|
|
|
65
|
|
|
66 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.
|
|
|
67
|
|
|
68 </token>
|
|
|
69
|
|
|
70 </macros>
|
