Mercurial > repos > yusuf > add_missing_coverage
comparison AddMissingCoverage.xml @ 0:a3129cb0af43 default tip
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author | Yusuf Ali <ali@yusuf.email> |
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date | Wed, 25 Mar 2015 13:02:25 -0600 |
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1 <?xml version="1.0"?> | |
2 | |
3 <tool id="hgvs_add_coverage" name="Add poor/missing coverage info"> | |
4 <description>to an annotated HGVS table</description> | |
5 <version_string>hgvs_add_missing_sample_coverage -v</version_string> | |
6 <command interpreter="perl">hgvs_add_missing_sample_coverage $input_hgvs_annotated_table $out_hgvs_annotated_table $sample_name $sample_bam $max_homo_fn_coverage $max_het_fn_coverage $min_mapq $min_baq</command> | |
7 <inputs> | |
8 <param format="achri_annotated_snp_table" name="input_hgvs_annotated_table" type="data" label="Annotated variant calls table with HGVS syntax"/> | |
9 <param name="sample_name" type="text" label="Name of sample to check for read coverage"/> | |
10 <param name="sample_bam" type="data" format="bam" label="Mapped reads to be checked (BAM format)" help="For each variant in the input table that does NOT include the specified sample name in the Sources column, this BAM file will be checked for concordant reads"/> | |
11 <param name="max_homo_fn_coverage" label="Minimum read coverage to exclude false negative homozygous variants" type="integer" min="1" value="3" /> | |
12 <param name="max_het_fn_coverage" label="Minimum read coverage to exclude false negative heterozygous variants" type="integer" min="1" value="20" /> | |
13 <param name="min_mapq" label="Minimum mapping quality score to consider a read" type="integer" min="1" value="20" help="(10=p-value 0.1, 20=p-value 0.01, etc.)"/> | |
14 <param name="min_baq" label="Minimum base quality score to consider a read" type="integer" min="1" value="20" help="(10=p-value 0.1, 20=p-value 0.01, etc.)"/> | |
15 </inputs> | |
16 <outputs> | |
17 <data format="achri_annotated_snp_table" name="out_hgvs_annotated_table" type="data" label="Variant table with poor/missing coverage data for ${sample_name}"/> | |
18 </outputs> | |
19 | |
20 <tests> | |
21 </tests> | |
22 | |
23 <help> | |
24 Once this tools is run, lack of the given sample name in a table row means the sample almost definitely does not contain the variant that row reports. | |
25 This tool adds a sample to the Sources column of the variant table if it is not already there, but the given BAM file either: | |
26 | |
27 1. has at least 1/max_het_fn_coverage read proportion supporting the variant (in which case the sample name is added with a "+"), or | |
28 | |
29 2. has fewer than max_homo_fn_coverage or max_het_fn_coverage reads mapped in total, and those reads neither conflict with nor support the variant called (in which case the sample name is added with a "~") | |
30 </help> | |
31 | |
32 </tool> |