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henrikstranneheim committed Feb 13, 2018
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8 changes: 4 additions & 4 deletions docs/vcfParser.rst
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vcfParser
=========
==========
Parses vcf files to reformat/add INFO fields and metaData headers and/or select entries
belonging to a subgroup e.g. a list of genes. Input can be piped or supplied as an infile.

Usage
-----
------
``vcfParser.pl infile.vcf > outfile.vcf``

``vcfParser.pl infile.vcf --parseVEP 1 -rf External_Db.txt -rf_ac 3 -sf genes.v1.0.txt -sf_mc 3 -sf_ac 3,4,11,15,17,20 -sof selected_genes.vcf > outfile.vcf``
Expand All @@ -15,7 +15,7 @@ vcfParser is written in Perl, so naturally you need to have Perl installed. The
module `Set::IntervalTree`_ is required and are used to add "ranged" annotations.

VEP
~~~
~~~~
Parses the output from VEP to include RefSeq transcripts. The transcript and protein
annotations, moste severe consequence and gene annotations are also included in the output
. Transcript protein predictions (Sift and Polyphen) can also be included.
Expand All @@ -26,7 +26,7 @@ A list of genes and their corresponding HGNC Symbol can be used to fork the anal
"selected" genes and "orphan" genes.

GuideLines on format for database of genes
********************************
*******************************************
- The database file should contain a header line starting with "#".
- The number of headers should match the number of field elements for each entry.
- Do not use whitespace in headers.
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