Mercurial > repos > blankenberg > naive_variant_detector

annotate tools/naive_variant_detector.xml @ 21:69d5400f3186 default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
update readme
author Daniel Blankenberg <dan@bx.psu.edu>
date Tue, 27 Aug 2013 14:54:49 -0400
parents 7f654ba273cb
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
eeb1103b8bd5 Update pyBamtools dependency revision.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 7
diff changeset
1 <tool id="naive_variant_detector" name="Naive Variant Caller" version="0.0.1">
10
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
2 <description>tabulate variable sites from BAM datasets</description>
1
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
3 <requirements>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
4 <requirement type="package" version="1.7.1">numpy</requirement>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
5 <requirement type="package" version="0.0.1">pyBamParser</requirement>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
6 <requirement type="package" version="0.0.1">pyBamTools</requirement>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
7 </requirements>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
8 <stdio>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
9 <exit_code range="1:" err_level="fatal" />
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
10 <exit_code range=":-1" err_level="fatal" />
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
11 </stdio>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
12 <command interpreter="python">naive_variant_detector.py
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
13 -o "${output_vcf}"
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
14
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
15 #for $input_bam in $reference_source.input_bams:
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
16 -b "${input_bam.input_bam}"
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
17 -i "${input_bam.input_bam.metadata.bam_index}"
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
18 #end for
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
19
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
20 #if $reference_source.reference_source_selector != "history":
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
21 -r "${reference_source.ref_file.fields.path}"
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
22 #elif $reference_source.ref_file:
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
23 -r "${reference_source.ref_file}"
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
24 #end if
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
25
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
26 #for $region in $regions:
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
27 --region "${region.chromosome}:${region.start}-${region.end}"
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
28 #end for
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
29
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
30 ${variants_only}
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
31
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
32 ${use_strand}
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
33
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
34 --ploidy "${$ploidy}"
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
35
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
36 --min_support_depth "${min_support_depth}"
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
37
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
38 #if str($min_base_quality):
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
39 --min_base_quality "${min_base_quality}"
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
40 #end if
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
41
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
42 #if str($min_mapping_quality):
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
43 --min_mapping_quality "${min_mapping_quality}"
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
44 #end if
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
45
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
46 --coverage_dtype "${coverage_dtype}"
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
47
5
4a67169be0ee Update to allow out of bounds positions to be not be fatal errors.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 4
diff changeset
48 --allow_out_of_bounds_positions
4a67169be0ee Update to allow out of bounds positions to be not be fatal errors.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 4
diff changeset
49
1
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
50 </command>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
51 <inputs>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
52 <conditional name="reference_source">
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
53 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
54 <option value="cached">Locally cached</option>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
55 <option value="history">History</option>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
56 </param>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
57 <when value="cached">
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
58 <repeat name="input_bams" title="BAM file" min="1" >
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
59 <param name="input_bam" type="data" format="bam" label="BAM file">
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
60 <validator type="unspecified_build" />
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
61 <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="value" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
62 </param>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
63 </repeat>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
64 <param name="ref_file" type="select" label="Using reference genome" >
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
65 <options from_data_table="sam_fa_indexes">
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
66 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...-->
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
67 </options>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
68 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
69 </param>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
70 </when>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
71 <when value="history"> <!-- FIX ME!!!! -->
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
72 <repeat name="input_bams" title="BAM file" min="1" >
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
73 <param name="input_bam" type="data" format="bam" label="BAM file" >
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
74 </param>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
75 </repeat>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
76 <param name="ref_file" type="data" format="fasta" label="Using reference file" optional="True" />
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
77 </when>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
78 </conditional>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
79
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
80 <repeat name="regions" title="Restrict to regions" min="0" >
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
81 <param name="chromosome" type="text" value="" optional="False" label="Chromosome" />
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
82 <param name="start" type="integer" value="" optional="True" label="Start" />
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
83 <param name="end" type="integer" value="" optional="True" label="End" />
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
84 </repeat>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
85
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
86 <!-- TODO: enhance filtering -->
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
87 <param name="min_support_depth" type="integer" value="0" min="0" label="Minimum number of reads needed to consider a REF/ALT" />
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
88 <param name="min_base_quality" type="integer" value="" label="Minimum base quality" optional="True" />
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
89 <param name="min_mapping_quality" type="integer" value="" label="Minimum mapping quality" optional="True" />
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
90
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
91 <param name="ploidy" type="integer" value="2" min="1" label="Ploidy" />
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
92 <param name="variants_only" type="boolean" truevalue="--variants_only" falsevalue="" checked="False" label="Only write out positions with with possible alternate alleles"/>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
93
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
94 <param name="use_strand" type="boolean" truevalue="--use_strand" falsevalue="" checked="False" label="Report counts by strand"/>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
95
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
96 <param name="coverage_dtype" type="select" label="Choose the dtype to use for storing coverage information" help="This affects the maximum recorded value for a position, e.g. uint8 would be 255 coverage, but will require the least amount of RAM">
10
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
97 <option value="uint8">uint8</option>
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
98 <option value="uint16" selected="True">uint16</option>
1
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
99 <option value="uint32">uint32</option>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
100 <option value="uint64">uint64</option>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
101 </param>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
102
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
103 </inputs>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
104 <outputs>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
105 <data format="vcf" name="output_vcf" />
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
106 </outputs>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
107 <help>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
108 **What it does**
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
109
10
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
110 This tool is a naive variant caller that processes aligned sequencing reads from the BAM format and produces a VCF file containing per position variant calls. This tool allows multiple BAM files to be provided as input and utilizes read group information to make calls for individual samples.
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
111
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
112 User configurable options allow filtering reads that do not pass mapping or base quality thresholds and minimum per base read depth; user's can also specify the ploidy and whether to consider each strand separately.
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
113
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
114 In addition to calling alternate alleles based upon simple ratios of nucleotides at a position, per base nucleotide counts are also provided. A custom tag, NC, is used within the Genotype fields. The NC field is a comma-separated listing of nucleotide counts in the form of &lt;nucleotide&gt;=&lt;count&gt;, where a plus or minus character is prepended to indicate strand, if the strandedness option was specified.
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
115
1
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
116
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
117 ------
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
118
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
119 **Inputs**
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
120
10
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
121 Accepts one or more BAM input files and a reference genome from the built-in list or from a FASTA file in your history.
1
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
122
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
123
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
124 **Outputs**
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
125
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
126 The output is in VCF format.
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
127
12
7f654ba273cb Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 11
diff changeset
128 Example VCF output line, without reporting by strand:
21
69d5400f3186 update readme
Daniel Blankenberg <dan@bx.psu.edu>
parents: 12
diff changeset
129 ``chrM 16029 . T G,A,C . . AC=15,9,5;AF=0.00155311658729,0.000931869952371,0.000517705529095 GT:AC:AF:NC 0/0:15,9,5:0.00155311658729,0.000931869952371,0.000517705529095:A=9,C=5,T=9629,G=15,``
12
7f654ba273cb Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 11
diff changeset
130
7f654ba273cb Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 11
diff changeset
131 Example VCF output line, when reporting by strand:
21
69d5400f3186 update readme
Daniel Blankenberg <dan@bx.psu.edu>
parents: 12
diff changeset
132 ``chrM 16029 . T G,A,C . . AC=15,9,5;AF=0.00155311658729,0.000931869952371,0.000517705529095 GT:AC:AF:NC 0/0:15,9,5:0.00155311658729,0.000931869952371,0.000517705529095:+T=3972,-A=9,-C=5,-T=5657,-G=15,``
12
7f654ba273cb Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 11
diff changeset
133
10
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
134 **Options**
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
135
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
136 Reference Genome:
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
137
21
69d5400f3186 update readme
Daniel Blankenberg <dan@bx.psu.edu>
parents: 12
diff changeset
138 Ensure that you have selected the correct reference genome, either from the list of built-in genomes or by selecting the corresponding FASTA file from your history.
10
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
139
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
140 Restrict to regions:
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
141
21
69d5400f3186 update readme
Daniel Blankenberg <dan@bx.psu.edu>
parents: 12
diff changeset
142 You can specify any number of regions on which you would like to receive results. You can specify just a chromosome name, or a chromosome name and start postion, or a chromosome name and start and end position for the set of desired regions.
10
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
143
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
144 Minimum number of reads needed to consider a REF/ALT:
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
145
21
69d5400f3186 update readme
Daniel Blankenberg <dan@bx.psu.edu>
parents: 12
diff changeset
146 This value declares the minimum number of reads containing a particular base at each position in order to list and use said allele in genotyping calls. Default is 0.
10
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
147
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
148 Minimum base quality:
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
149
21
69d5400f3186 update readme
Daniel Blankenberg <dan@bx.psu.edu>
parents: 12
diff changeset
150 The minimum base quality score needed for the position in a read to be used for nucleotide counts and genotyping. Default is no filter.
10
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
151
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
152 Minimum mapping quality:
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
153
21
69d5400f3186 update readme
Daniel Blankenberg <dan@bx.psu.edu>
parents: 12
diff changeset
154 The minimum mapping quality score needed to consider a read for nucleotide counts and genotyping. Default is no filter.
10
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
155
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
156 Ploidy:
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
157
21
69d5400f3186 update readme
Daniel Blankenberg <dan@bx.psu.edu>
parents: 12
diff changeset
158 The number of genotype calls to make at each reported position.
10
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
159
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
160 Only write out positions with with possible alternate alleles:
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
161
21
69d5400f3186 update readme
Daniel Blankenberg <dan@bx.psu.edu>
parents: 12
diff changeset
162 When set, only positions which have at least one non-reference nucleotide which passes declare filters will be present in the output.
10
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
163
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
164 Report counts by strand:
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
165
21
69d5400f3186 update readme
Daniel Blankenberg <dan@bx.psu.edu>
parents: 12
diff changeset
166 When set, nucleotide counts (NC) will be reported in reference to the aligned read's source strand. Reported as: &lt;strand&gt;&lt;BASE&gt;=&lt;COUNT&gt;.
10
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
167
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
168 Choose the dtype to use for storing coverage information:
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
169
21
69d5400f3186 update readme
Daniel Blankenberg <dan@bx.psu.edu>
parents: 12
diff changeset
170 This controls the maximum depth value for each nucleotide/position/strand (when specified). Smaller values require the least amount of memory, but have smaller maximal limits.
10
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
171
21
69d5400f3186 update readme
Daniel Blankenberg <dan@bx.psu.edu>
parents: 12
diff changeset
172 +--------+----------------------------+
69d5400f3186 update readme
Daniel Blankenberg <dan@bx.psu.edu>
parents: 12
diff changeset
173 | name | maximum coverage value |
69d5400f3186 update readme
Daniel Blankenberg <dan@bx.psu.edu>
parents: 12
diff changeset
174 +========+============================+
69d5400f3186 update readme
Daniel Blankenberg <dan@bx.psu.edu>
parents: 12
diff changeset
175 | uint8 | 255 |
69d5400f3186 update readme
Daniel Blankenberg <dan@bx.psu.edu>
parents: 12
diff changeset
176 +--------+----------------------------+
69d5400f3186 update readme
Daniel Blankenberg <dan@bx.psu.edu>
parents: 12
diff changeset
177 | uint16 | 65,535 |
69d5400f3186 update readme
Daniel Blankenberg <dan@bx.psu.edu>
parents: 12
diff changeset
178 +--------+----------------------------+
69d5400f3186 update readme
Daniel Blankenberg <dan@bx.psu.edu>
parents: 12
diff changeset
179 | uint32 | 4,294,967,295 |
69d5400f3186 update readme
Daniel Blankenberg <dan@bx.psu.edu>
parents: 12
diff changeset
180 +--------+----------------------------+
69d5400f3186 update readme
Daniel Blankenberg <dan@bx.psu.edu>
parents: 12
diff changeset
181 | uint64 | 18,446,744,073,709,551,615 |
69d5400f3186 update readme
Daniel Blankenberg <dan@bx.psu.edu>
parents: 12
diff changeset
182 +--------+----------------------------+
10
d6d7aa386bad Update help text.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 8
diff changeset
183
1
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
184 ------
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
185
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
186 **Citation**
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
187
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
188 If you use this tool, please cite Blankenberg D, et al. *In preparation.*
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
189
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
190 </help>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
191 <tests>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
192 <test>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
193 <param name="reference_source_selector" value="history" />
4
1c23da12b768 Remove test-data/ path from defined Tool tests.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 1
diff changeset
194 <param name="input_bam" value="fake_phiX174_reads_1.bam" ftype="bam" />
1c23da12b768 Remove test-data/ path from defined Tool tests.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 1
diff changeset
195 <param name="ref_file" value="phiX174.fasta" ftype="fasta" />
7
5907f90b7ae1 Fix test.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 5
diff changeset
196 <param name="regions" value="0" />
1
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
197 <param name="min_support_depth" value="0" />
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
198 <param name="min_base_quality" value="" />
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
199 <param name="min_mapping_quality" value="" />
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
200 <param name="ploidy" value="2" />
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
201 <param name="variants_only" value="False" />
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
202 <param name="use_strand" value="False" />
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
203 <param name="coverage_dtype" value="uint8" />
4
1c23da12b768 Remove test-data/ path from defined Tool tests.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 1
diff changeset
204 <output name="output_vcf" file="fake_phiX174_reads_1_test_out_1.vcf" compare="contains" />
1
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
205 </test>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
206 </tests>
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
207
55b4460cd0ce Add naive variant detector tool.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
208 </tool>