Mercurial > repos > peterjc > coverage_stats
comparison coverage_stats-1b5523d3d2c2/tools/coverage_stats/coverage_stats.xml @ 3:57b3ea22aff3 draft
Uploaded v0.1.0 which was already on the Test Tool Shed. Included Python 3 support.
author | peterjc |
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date | Tue, 11 Aug 2020 18:23:05 -0400 |
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2:7254ece0c0ff | 3:57b3ea22aff3 |
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1 <tool id="coverage_stats" name="BAM coverage statistics" version="0.1.0"> | |
2 <description>using samtools idxstats and depth</description> | |
3 <requirements> | |
4 <requirement type="package" version="1.4.1">samtools</requirement> | |
5 </requirements> | |
6 <version_command> | |
7 python $__tool_directory__/coverage_stats.py --version | |
8 </version_command> | |
9 <command detect_errors="aggressive"> | |
10 python $__tool_directory__/coverage_stats.py | |
11 -b '$input_bam' | |
12 -i '${input_bam.metadata.bam_index}' | |
13 -o '$out_tabular' | |
14 -d '$max_depth' | |
15 </command> | |
16 <inputs> | |
17 <param name="input_bam" type="data" format="bam" label="Input BAM file" /> | |
18 <param name="max_depth" type="integer" min="0" max="10000000" label="Max depth" value="8000" /> | |
19 </inputs> | |
20 <outputs> | |
21 <data name="out_tabular" format="tabular" label="$input_bam.name (coverage stats)" /> | |
22 </outputs> | |
23 <tests> | |
24 <test> | |
25 <param name="input_bam" value="ex1.bam" ftype="bam" /> | |
26 <param name="max_depth" value="123" /> | |
27 <output name="out_tabular" file="ex1.coverage_stats.tabular" ftype="tabular" /> | |
28 </test> | |
29 <test> | |
30 <param name="input_bam" value="ex1.bam" ftype="bam" /> | |
31 <param name="max_depth" value="50" /> | |
32 <output name="out_tabular" file="ex1.coverage_stats.md50.tabular" ftype="tabular" /> | |
33 </test> | |
34 <test> | |
35 <param name="input_bam" value="coverage_test.bam" ftype="bam" /> | |
36 <param name="max_depth" value="123" /> | |
37 <output name="out_tabular" file="coverage_test.coverage_stats.tabular" ftype="tabular" /> | |
38 </test> | |
39 </tests> | |
40 <help> | |
41 **What it does** | |
42 | |
43 This tool runs the commands ``samtools idxstats`` and ``samtools depth`` from the | |
44 SAMtools toolkit, and parses their output to produce a consise summary of the | |
45 coverage information for each reference sequence. | |
46 | |
47 Input is a sorted and indexed BAM file, the output is tabular. The first four | |
48 columns match the output from ``samtools idxstats``, the additional columns are | |
49 calculated from the ``samtools depth`` output. The final row with a star as the | |
50 reference identifier represents unmapped reads, and will have zeros in every | |
51 column except columns one and four. | |
52 | |
53 ====== ================================================================================= | |
54 Column Description | |
55 ------ --------------------------------------------------------------------------------- | |
56 1 Reference sequence identifier | |
57 2 Reference sequence length | |
58 3 Number of mapped reads | |
59 4 Number of placed but unmapped reads (typically unmapped partners of mapped reads) | |
60 5 Minimum coverage (per base of reference) | |
61 6 Maximum coverage (per base of reference) | |
62 7 Mean coverage (given to 2 dp) | |
63 ====== ================================================================================= | |
64 | |
65 Example output from a *de novo* assembly: | |
66 | |
67 ========== ====== ====== ====== ======= ======= ======== | |
68 identiifer length mapped placed min_cov max_cov mean_cov | |
69 ---------- ------ ------ ------ ------- ------- -------- | |
70 contig_1 833604 436112 0 1 157 71.95 | |
71 contig_2 14820 9954 0 1 152 91.27 | |
72 contig_3 272099 142958 0 1 150 72.31 | |
73 contig_4 135519 73288 0 1 149 75.23 | |
74 contig_5 91245 46759 0 1 157 70.92 | |
75 contig_6 175604 95744 0 1 146 75.99 | |
76 contig_7 90586 48158 0 1 151 72.93 | |
77 contig_9 234347 126458 0 1 159 75.40 | |
78 contig_10 121515 60211 0 1 152 68.12 | |
79 ... ... ... ... ... ... ... | |
80 contig_604 712 85 0 1 49 21.97 | |
81 \* 0 0 950320 0 0 0.00 | |
82 ========== ====== ====== ====== ======= ======= ======== | |
83 | |
84 In this example there were 604 contigs, each with one line in the output table, | |
85 plus the final row (labelled with an asterisk) representing 950320 unmapped reads. | |
86 In this BAM file, the fourth column was otherwise zero. | |
87 | |
88 .. class:: warningmark | |
89 | |
90 **Note**. If using this on a mapping BAM file, beware that the coverage counting is | |
91 done per base of the reference. This means if your reference has any extra bases | |
92 compared to the reads being mapped, those bases will be skipped by CIGAR D operators | |
93 and these "extra" bases can have an extremely low coverage, giving a potentially | |
94 misleading ``min_cov`` values. A sliding window coverage may be more appropriate. | |
95 | |
96 **Note**. Up until samtools 1.2, there was an internal hard limit of 8000 for the | |
97 pileup routine, meaning the reported coverage from ``samtools depth`` would show | |
98 maximum coverage depths *around* 8000. This is now a run time option. | |
99 | |
100 | |
101 **Citation** | |
102 | |
103 If you use this Galaxy tool in work leading to a scientific publication please | |
104 cite: | |
105 | |
106 Heng Li et al (2009). The Sequence Alignment/Map format and SAMtools. | |
107 Bioinformatics 25(16), 2078-9. | |
108 https://doi.org/10.1093/bioinformatics/btp352 | |
109 | |
110 Peter J.A. Cock (2013), BAM coverage statistics using samtools idxstats and depth. | |
111 http://toolshed.g2.bx.psu.edu/view/peterjc/coverage_stats | |
112 | |
113 This wrapper is available to install into other Galaxy Instances via the Galaxy | |
114 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/coverage_stats | |
115 </help> | |
116 <citations> | |
117 <citation type="doi">10.1093/bioinformatics/btp352</citation> | |
118 </citations> | |
119 </tool> |