Provided by: pbgenomicconsensus_2.3.2-5_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
(http://www.sequenceontology.org/gff3.shtml). 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 referred 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 Name Description Example
Number
1 seqId The full FASTA header for the lambda_NEB3011
reference contig.
2 source (unused; always populated with .) .
3 type the type of variant. One of substitution
insertion, deletion, or
substitution.
4 start 1-based start coordinate for the 200
variant.
5 end 1-based end coordinate for the 215
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 probability 37
that the variant is real,
rounded to the nearest integer
and truncated at 93
reference the reference base or bases for T, .
the variant site. May be . to
represent a zero-length
substring (for insertion
events)
variantSeq the read base or bases
corresponding to the variant. T (haploid);
. encodes a zer-length string,
as for a deletion. T/C, T/.
(heterozygous)
frequency the read coverage of the
variant itself; for 13 (haploid)
heterozygous variants, the
frequency of both observed 15/12 (heterozygous)
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.
AUTHORS
Pacific Biosciences <devnet@pacificbiosciences.com>.