Provided by: pbgenomicconsensus_2.1.0-1_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 (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 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 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 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 T (haploid);
corresponding to the
variant. . encodes a T/C, T/.
zer-length string, as (heterozygous)
for a deletion.
frequency the read coverage of the 13 (haploid)
variant itself; for
heterozygous variants, 15/12 (heterozygous)
the frequency of both
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.
AUTHORS
Pacific Biosciences <devnet@pacificbiosciences.com>.