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.
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 header for the reference contig. |
lambda_NEB3011 |
|
| 2 |
source |
(unused; always populated with .) |
. |
|
| 3 |
type |
the type of variant. One of insertion, deletion, or
substitution. |
substitution |
|
| 4 |
start |
1-based start coordinate for the variant. |
200 |
|
| 5 |
end |
1-based end coordinate for the variant. start<=end always obtains,
regardless of strand. |
215 |
|
| 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 variant site (not the variant itself) |
42 |
|
| confidence |
the phred-scaled probability that the variant is real, rounded to the
nearest integer and truncated at 93 |
37 |
|
| reference |
the reference base or bases for the variant site. May be . to
represent a zero-length substring (for insertion events) |
T, . |
|
| variantSeq |
the read base or bases corresponding to the variant. . encodes a
zer-length string, as for a deletion. |
0.0 T (haploid); T/C, T/. (heterozygous) 168u |
|
| frequency |
the read coverage of the variant itself; for heterozygous variants, the
frequency of both observed alleles. This is an optional field. |
0.0 13 (haploid) 15/12 (heterozygous) 168u |
|
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>
