Provided by: pbgenomicconsensus_2.0.0+20151210-1_all 
NAME
pbgff - Pacific Biosciences extended GFFv3 file format
DESCRIPTION
As of this version, variants.gff is our primary variant call file format. The
variants.gff file is based on the GFFv3 standard. The GFFv3 standard describes a
tab-delimited plain-text file meta-format for describing genomic "features." Each gff
file consists of some initial "header" lines supplying metadata, and then a number of
"feature" lines providing information about each identified variant.
The GFF Coordinate System
All coordinates in GFF files are 1-based, and all intervals start, end are understood as
including both endpoints.
Headers
The variants.gff file begins with a block of metadata headers, which looks like the
following:
##gff-version 3
##pacbio-variant-version 2.1
##date Tue Feb 28 17:44:18 2012
##feature-ontology http://song.cvs.sourceforge.net/*checkout*/song/ontology/sofa.obo?revision=1.12
##source GenomicConsensus v0.1.0
##source-commandline callVariants.py --algorithm=plurality aligned_reads.cmp.h5 -r spinach.fasta -o variants.gff
##source-alignment-file /home/popeye/data/aligned_reads.cmp.h5
##source-reference-file /home/popeye/data/spinach.fasta
##sequence-region EGFR_Exon_23 1 189
##sequence-header EGFR_Exon_24 1 200
The source and source-commandline describe the name and version of the software generating
the file. pacbio-variant-version reflects the specification version that the file
contents should adhere to.
The sequence-region headers describe the names and extents of the reference groups (i.e.
reference contigs) that will be refered to in the file. The names are the same as the
full FASTA header.
source-alignment-file and source-reference-file record absolute paths to the primary input
files.
Feature lines
After the headers, each line in the file describes a genomic feature; in this file, all
the features are potential variants flagged by the variant caller. The general format of
a variant line is a 9-column (tab-delimited) record, where the first 8 columns correspond
to fixed, predefined entities in the GFF standard, while the 9th column is a flexible
semicolon-delimited list of mappings key=value.
The 8 predefined columns are as follows:
┌──────────────┬────────┬─────────────────────┬────────────────┐
│Column Number │ Name │ Description │ Example │
├──────────────┼────────┼─────────────────────┼────────────────┤
│1 │ seqId │ The full FASTA │ lambda_NEB3011 │
│ │ │ header for the │ │
│ │ │ reference contig. │ │
├──────────────┼────────┼─────────────────────┼────────────────┤
│2 │ source │ (unused; always │ . │
│ │ │ populated with .) │ │
└──────────────┴────────┴─────────────────────┴────────────────┘
│3 │ type │ the type of │ substitution │
│ │ │ variant. One of │ │
│ │ │ insertion, │ │
│ │ │ deletion, or │ │
│ │ │ substitution. │ │
├──────────────┼────────┼─────────────────────┼────────────────┤
│4 │ start │ 1-based start │ 200 │
│ │ │ coordinate for the │ │
│ │ │ variant. │ │
├──────────────┼────────┼─────────────────────┼────────────────┤
│5 │ end │ 1-based end │ 215 │
│ │ │ coordinate for the │ │
│ │ │ variant. │ │
│ │ │ start<=end always │ │
│ │ │ obtains, regardless │ │
│ │ │ of strand. │ │
├──────────────┼────────┼─────────────────────┼────────────────┤
│6 │ score │ unused; populated │ . │
│ │ │ with . │ │
├──────────────┼────────┼─────────────────────┼────────────────┤
│7 │ strand │ unused; populated │ . │
│ │ │ with . │ │
├──────────────┼────────┼─────────────────────┼────────────────┤
│8 │ phase │ unused; populated │ . │
│ │ │ with . │ │
└──────────────┴────────┴─────────────────────┴────────────────┘
The attributes in the 9th (final) column are as follows:
┌───────────┬──────────────────────────┬──────────────────────────────┐
│Key │ Description │ Example value │
├───────────┼──────────────────────────┼──────────────────────────────┤
│coverage │ the read coverage of the │ 42 │
│ │ variant site (not the │ │
│ │ variant itself) │ │
├───────────┼──────────────────────────┼──────────────────────────────┤
│confidence │ the phred-scaled │ 37 │
│ │ probability that the │ │
│ │ variant is real, rounded │ │
│ │ to the nearest integer │ │
│ │ and truncated at 93 │ │
├───────────┼──────────────────────────┼──────────────────────────────┤
│reference │ the reference base or │ T, . │
│ │ bases for the variant │ │
│ │ site. May be . to │ │
│ │ represent a zero-length │ │
│ │ substring (for insertion │ │
│ │ events) │ │
├───────────┼──────────────────────────┼──────────────────────────────┤
│variantSeq │ the read base or bases │ │
│ │ corresponding to the │ T (haploid); │
│ │ variant. . encodes a │ │
│ │ zer-length string, as │ T/C, T/. │
│ │ for a deletion. │ (heterozygous) │
├───────────┼──────────────────────────┼──────────────────────────────┤
│frequency │ the read coverage of the │ │
│ │ variant itself; for │ 13 (haploid) │
│ │ heterozygous variants, │ │
│ │ the frequency of both │ 15/12 (heterozygous) │
│ │ observed alleles. This │ │
│ │ is an optional field. │ │
└───────────┴──────────────────────────┴──────────────────────────────┘
The attributes may be present in any order.
The four types of variant we support are as follows. (Recall that the field separator is a
tab, not a space.)
1. Insertion. Examples:
ref00001 . insertion 8 8 . . . reference=.;variantSeq=G;confidence=22;coverage=18;frequency=10
ref00001 . insertion 19 19 . . . reference=.;variantSeq=G/.;confidence=22;coverage=18;frequency=7/5
For insertions, start==end, and the insertion event is understood as taking place
following the reference position start.
2. Deletion. Examples:
ref00001 . deletion 348 349 . . . reference=G;variantSeq=.;confidence=39;coverage=25;frequency=20
ref00001 . deletion 441 443 . . . reference=GG;variantSeq=GG/.;confidence=39;coverage=25;frequency=8/8
3. Substitution. Examples:
ref000001 . substitution 100 102 . . . reference=GGG;variantSeq=CCC;confidence=50;coverage=20;frequency=16
ref000001 . substitution 200 201 . . . reference=G;variantSeq=G/C;confidence=50;coverage=20;frequency=10/6
Compression
The gff metaformat is verbose, so for practical purposes we will gzip encode variants.gff
files as variants.gff.gz. Consumers of the variant file should be able to read it in
either form.
SEE ALSO
The VCF and BED standards describe variant-call specific file formats. We can currently
translate variants.gff files to these formats, but they are not the primary output of the
variant callers.
AUTHOR
Pacific Biosciences <devnet@pacificbiosciences.com>