Mercurial > repos > peterjc > coverage_stats
annotate tools/coverage_stats/coverage_stats.xml @ 2:7254ece0c0ff draft
v0.0.5 - Supports max coverage depth in recent samtools. Expects samtools 1.4.1 via Conda, not via Tool Shed.
| author | peterjc |
|---|---|
| date | Thu, 11 May 2017 12:16:10 -0400 |
| parents | d1fdfaae5dbe |
| children |
| rev | line source |
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7254ece0c0ff
v0.0.5 - Supports max coverage depth in recent samtools. Expects samtools 1.4.1 via Conda, not via Tool Shed.
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1 <tool id="coverage_stats" name="BAM coverage statistics" version="0.0.5"> |
| 0 | 2 <description>using samtools idxstats and depth</description> |
| 3 <requirements> | |
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v0.0.5 - Supports max coverage depth in recent samtools. Expects samtools 1.4.1 via Conda, not via Tool Shed.
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4 <requirement type="package" version="1.4.1">samtools</requirement> |
| 0 | 5 </requirements> |
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v0.0.5 - Supports max coverage depth in recent samtools. Expects samtools 1.4.1 via Conda, not via Tool Shed.
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6 <version_command> |
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7254ece0c0ff
v0.0.5 - Supports max coverage depth in recent samtools. Expects samtools 1.4.1 via Conda, not via Tool Shed.
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7 python $__tool_directory__/coverage_stats.py --version |
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7254ece0c0ff
v0.0.5 - Supports max coverage depth in recent samtools. Expects samtools 1.4.1 via Conda, not via Tool Shed.
peterjc
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8 </version_command> |
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7254ece0c0ff
v0.0.5 - Supports max coverage depth in recent samtools. Expects samtools 1.4.1 via Conda, not via Tool Shed.
peterjc
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9 <command detect_errors="aggressive"> |
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7254ece0c0ff
v0.0.5 - Supports max coverage depth in recent samtools. Expects samtools 1.4.1 via Conda, not via Tool Shed.
peterjc
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10 python $__tool_directory__/coverage_stats.py '$input_bam' '${input_bam.metadata.bam_index}' '$out_tabular' '$max_depth' |
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7254ece0c0ff
v0.0.5 - Supports max coverage depth in recent samtools. Expects samtools 1.4.1 via Conda, not via Tool Shed.
peterjc
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11 </command> |
| 0 | 12 <inputs> |
| 13 <param name="input_bam" type="data" format="bam" label="Input BAM file" /> | |
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7254ece0c0ff
v0.0.5 - Supports max coverage depth in recent samtools. Expects samtools 1.4.1 via Conda, not via Tool Shed.
peterjc
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14 <param name="max_depth" type="integer" min="0" max="10000000" label="Max depth" value="8000" /> |
| 0 | 15 </inputs> |
| 16 <outputs> | |
| 17 <data name="out_tabular" format="tabular" label="$input_bam.name (coverage stats)" /> | |
| 18 </outputs> | |
| 19 <tests> | |
| 20 <test> | |
| 21 <param name="input_bam" value="ex1.bam" ftype="bam" /> | |
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7254ece0c0ff
v0.0.5 - Supports max coverage depth in recent samtools. Expects samtools 1.4.1 via Conda, not via Tool Shed.
peterjc
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22 <param name="max_depth" value="123" /> |
| 0 | 23 <output name="out_tabular" file="ex1.coverage_stats.tabular" ftype="tabular" /> |
| 24 </test> | |
| 25 <test> | |
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7254ece0c0ff
v0.0.5 - Supports max coverage depth in recent samtools. Expects samtools 1.4.1 via Conda, not via Tool Shed.
peterjc
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26 <param name="input_bam" value="ex1.bam" ftype="bam" /> |
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7254ece0c0ff
v0.0.5 - Supports max coverage depth in recent samtools. Expects samtools 1.4.1 via Conda, not via Tool Shed.
peterjc
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27 <param name="max_depth" value="50" /> |
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7254ece0c0ff
v0.0.5 - Supports max coverage depth in recent samtools. Expects samtools 1.4.1 via Conda, not via Tool Shed.
peterjc
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28 <output name="out_tabular" file="ex1.coverage_stats.md50.tabular" ftype="tabular" /> |
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7254ece0c0ff
v0.0.5 - Supports max coverage depth in recent samtools. Expects samtools 1.4.1 via Conda, not via Tool Shed.
peterjc
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29 </test> |
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7254ece0c0ff
v0.0.5 - Supports max coverage depth in recent samtools. Expects samtools 1.4.1 via Conda, not via Tool Shed.
peterjc
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30 <test> |
| 0 | 31 <param name="input_bam" value="coverage_test.bam" ftype="bam" /> |
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7254ece0c0ff
v0.0.5 - Supports max coverage depth in recent samtools. Expects samtools 1.4.1 via Conda, not via Tool Shed.
peterjc
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32 <param name="max_depth" value="123" /> |
| 0 | 33 <output name="out_tabular" file="coverage_test.coverage_stats.tabular" ftype="tabular" /> |
| 34 </test> | |
| 35 </tests> | |
| 36 <help> | |
| 37 **What it does** | |
| 38 | |
| 39 This tool runs the commands ``samtools idxstats`` and ``samtools depth`` from the | |
| 40 SAMtools toolkit, and parses their output to produce a consise summary of the | |
| 41 coverage information for each reference sequence. | |
| 42 | |
| 43 Input is a sorted and indexed BAM file, the output is tabular. The first four | |
| 44 columns match the output from ``samtools idxstats``, the additional columns are | |
| 45 calculated from the ``samtools depth`` output. The final row with a star as the | |
| 46 reference identifier represents unmapped reads, and will have zeros in every | |
| 47 column except columns one and four. | |
| 48 | |
| 49 ====== ================================================================================= | |
| 50 Column Description | |
| 51 ------ --------------------------------------------------------------------------------- | |
| 52 1 Reference sequence identifier | |
| 53 2 Reference sequence length | |
| 54 3 Number of mapped reads | |
| 55 4 Number of placed but unmapped reads (typically unmapped partners of mapped reads) | |
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7254ece0c0ff
v0.0.5 - Supports max coverage depth in recent samtools. Expects samtools 1.4.1 via Conda, not via Tool Shed.
peterjc
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56 5 Minimum coverage (per base of reference) |
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7254ece0c0ff
v0.0.5 - Supports max coverage depth in recent samtools. Expects samtools 1.4.1 via Conda, not via Tool Shed.
peterjc
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57 6 Maximum coverage (per base of reference) |
| 0 | 58 7 Mean coverage (given to 2 dp) |
| 59 ====== ================================================================================= | |
| 60 | |
| 61 Example output from a *de novo* assembly: | |
| 62 | |
| 63 ========== ====== ====== ====== ======= ======= ======== | |
| 64 identiifer length mapped placed min_cov max_cov mean_cov | |
| 65 ---------- ------ ------ ------ ------- ------- -------- | |
| 66 contig_1 833604 436112 0 1 157 71.95 | |
| 67 contig_2 14820 9954 0 1 152 91.27 | |
| 68 contig_3 272099 142958 0 1 150 72.31 | |
| 69 contig_4 135519 73288 0 1 149 75.23 | |
| 70 contig_5 91245 46759 0 1 157 70.92 | |
| 71 contig_6 175604 95744 0 1 146 75.99 | |
| 72 contig_7 90586 48158 0 1 151 72.93 | |
| 73 contig_9 234347 126458 0 1 159 75.40 | |
| 74 contig_10 121515 60211 0 1 152 68.12 | |
| 75 ... ... ... ... ... ... ... | |
| 76 contig_604 712 85 0 1 49 21.97 | |
| 77 \* 0 0 950320 0 0 0.00 | |
| 78 ========== ====== ====== ====== ======= ======= ======== | |
| 79 | |
| 80 In this example there were 604 contigs, each with one line in the output table, | |
| 81 plus the final row (labelled with an asterisk) representing 950320 unmapped reads. | |
| 82 In this BAM file, the fourth column was otherwise zero. | |
| 83 | |
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Uploaded v0.0.1b with warning about samtools 8000 coverage limit
peterjc
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84 .. class:: warningmark |
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d1fdfaae5dbe
Uploaded v0.0.1b with warning about samtools 8000 coverage limit
peterjc
parents:
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85 |
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7254ece0c0ff
v0.0.5 - Supports max coverage depth in recent samtools. Expects samtools 1.4.1 via Conda, not via Tool Shed.
peterjc
parents:
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diff
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86 **Note**. If using this on a mapping BAM file, beware that the coverage counting is |
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7254ece0c0ff
v0.0.5 - Supports max coverage depth in recent samtools. Expects samtools 1.4.1 via Conda, not via Tool Shed.
peterjc
parents:
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diff
changeset
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87 done per base of the reference. This means if your reference has any extra bases |
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7254ece0c0ff
v0.0.5 - Supports max coverage depth in recent samtools. Expects samtools 1.4.1 via Conda, not via Tool Shed.
peterjc
parents:
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diff
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88 compared to the reads being mapped, those bases will be skipped by CIGAR D operators |
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7254ece0c0ff
v0.0.5 - Supports max coverage depth in recent samtools. Expects samtools 1.4.1 via Conda, not via Tool Shed.
peterjc
parents:
1
diff
changeset
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89 and these "extra" bases can have an extremely low coverage, giving a potentially |
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7254ece0c0ff
v0.0.5 - Supports max coverage depth in recent samtools. Expects samtools 1.4.1 via Conda, not via Tool Shed.
peterjc
parents:
1
diff
changeset
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90 misleading ``min_cov`` values. A sliding window coverage may be more appropriate. |
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7254ece0c0ff
v0.0.5 - Supports max coverage depth in recent samtools. Expects samtools 1.4.1 via Conda, not via Tool Shed.
peterjc
parents:
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91 |
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7254ece0c0ff
v0.0.5 - Supports max coverage depth in recent samtools. Expects samtools 1.4.1 via Conda, not via Tool Shed.
peterjc
parents:
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92 **Note**. Up until samtools 1.2, there was an internal hard limit of 8000 for the |
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7254ece0c0ff
v0.0.5 - Supports max coverage depth in recent samtools. Expects samtools 1.4.1 via Conda, not via Tool Shed.
peterjc
parents:
1
diff
changeset
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93 pileup routine, meaning the reported coverage from ``samtools depth`` would show |
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7254ece0c0ff
v0.0.5 - Supports max coverage depth in recent samtools. Expects samtools 1.4.1 via Conda, not via Tool Shed.
peterjc
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94 maximum coverage depths *around* 8000. This is now a run time option. |
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d1fdfaae5dbe
Uploaded v0.0.1b with warning about samtools 8000 coverage limit
peterjc
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95 |
| 0 | 96 |
| 97 **Citation** | |
| 98 | |
| 99 If you use this Galaxy tool in work leading to a scientific publication please | |
| 100 cite: | |
| 101 | |
| 102 Heng Li et al (2009). The Sequence Alignment/Map format and SAMtools. | |
| 103 Bioinformatics 25(16), 2078-9. | |
| 104 http://dx.doi.org/10.1093/bioinformatics/btp352 | |
| 105 | |
| 106 Peter J.A. Cock (2013), BAM coverage statistics using samtools idxstats and depth. | |
| 107 http://toolshed.g2.bx.psu.edu/view/peterjc/coverage_stats | |
| 108 | |
| 109 This wrapper is available to install into other Galaxy Instances via the Galaxy | |
| 110 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/coverage_stats | |
| 111 </help> | |
| 112 <citations> | |
| 113 <citation type="doi">10.1093/bioinformatics/btp352</citation> | |
| 114 </citations> | |
| 115 </tool> |