gffread - GFF/GTF utility providing format conversions, region
filtering, FASTA sequence extraction
gffread <input_gff> [-g <genomic_seqs_fasta> |
<dir>][-s <seq_info.fsize>] [-o <outfile.gff>] [-t
<tname>] [-r [[<strand>]<chr>:]<start>..<end>
[-R]] [-CTVNJMKQAFPGUBHZWTOLE] [-w <exons.fa>] [-x <cds.fa>] [-y
<tr_cds.fa>] [-i <maxintron>] [--sort-by
<refseq_list.txt>]
- Filter and convert GFF3/GTF2 records, extract corresponding sequences etc.
By default (i.e. without -O) only process transcripts, ignore other
features.
- <input_gff> is a GFF file, use '-' for stdin
- -i
- discard transcripts having an intron larger than <maxintron>
- -l
- discard transcripts shorter than <minlen> bases
- -r
- only show transcripts overlapping coordinate range
<start>..<end> (on chromosome/contig <chr>, strand
<strand> if provided)
- -R
- for -r option, discard all transcripts that are not fully contained
within the given range
- -U
- discard single-exon transcripts
- -C
- coding only: discard mRNAs that have no CDS features
--nc non-coding only: discard mRNAs that have CDS
features
--ignore-locus : discard locus features and attributes
found in the input
- -A
- use the description field from <seq_info.fsize> and add it as the
value for a 'descr' attribute to the GFF record
- -s
- <seq_info.fsize> is a tab-delimited file providing this info for
each of the mapped sequences: <seq-name> <seq-length>
<seq-description> (useful for -A option with mRNA/EST/protein
mappings)
Sorting: (by default, chromosomes are kept in the order they were
found)
--sort-alpha : chromosomes (reference sequences) are
sorted alphabetically
--sort-by : sort the reference sequences by the order in
which their
- names are given in the <refseq.lst> file
- -F
- attempt to preserve all GFF attributes preservation
--keep-exon-attrs : for -F option, do not attempt
to reduce redundant
- exon/CDS attributes
- -G
- do not keep exon attributes, move them to the transcript feature (for GFF3
output)
--keep-genes : in transcript-only mode (default), also
preserve gene records
--keep-comments: for GFF3 input/output, try to preserve
comments
- -O
- process other non-transcript GFF records (by default non-transcript
records are ignored)
- -V
- discard any mRNAs with CDS having in-frame stop codons (requires
-g)
- -H
- for -V option, check and adjust the starting CDS phase if the
original phase leads to a translation with an in-frame stop codon
- -B
- for -V option, single-exon transcripts are also checked on the
opposite strand (requires -g)
- -P
- add transcript level GFF attributes about the coding status of each
transcript, including partialness or in-frame stop codons (requires
-g)
--add-hasCDS : add a "hasCDS" attribute with
value "true" for transcripts
- that have CDS features
--adj-stop stop codon adjustment: enables -P and
performs automatic
- adjustment of the CDS stop coordinate if premature or downstream
- -N
- discard multi-exon mRNAs that have any intron with a non-canonical splice
site consensus (i.e. not GT-AG, GC-AG or AT-AC)
- -J
- discard any mRNAs that either lack initial START codon or the terminal
STOP codon, or have an in-frame stop codon (i.e. only print mRNAs with a
complete CDS)
--no-pseudo: filter out records matching the 'pseudo'
keyword
--in-bed: input should be parsed as BED format
(automatic if the input
- filename ends with .bed*)
--in-tlf: input GFF-like one-line-per-transcript format
without exon/CDS
- features (see --tlf option below); automatic if the input filename
ends with .tlf)
-M/--merge : cluster the input transcripts into loci,
discarding
- "duplicated" transcripts (those with the same exact introns and
fully contained or equal boundaries)
-d <dupinfo> : for -M option, write
duplication info to file <dupinfo>
--cluster-only: same as -M/--merge but without
discarding any of the
- "duplicate" transcripts, only create "locus"
features
- -K
- for -M option: also discard as redundant the shorter, fully
contained
- transcripts (intron chains matching a part of the container)
- -Q
- for -M option, no longer require boundary containment when
assessing redundancy (can be combined with -K); only introns have
to match for multi-exon transcripts, and >=80% overlap for single-exon
transcripts
- -Y
- for -M option, enforce -Q but also discard overlapping
single-exon transcripts, even on the opposite strand (can be combined with
-K)
--force-exons: make sure that the lowest level GFF
features are considered
- "exon" features
--gene2exon: for single-line genes not parenting any
transcripts, add an
- exon feature spanning the entire gene (treat it as a transcript)
- -D
- decode url encoded characters within attributes
- -Z
- merge very close exons into a single exon (when intron size<4)
- -g
- full path to a multi-fasta file with the genomic sequences for all input
mappings, OR a directory with single-fasta files (one per genomic
sequence, with file names matching sequence names)
- -w
- write a fasta file with spliced exons for each GFF transcript
- -x
- write a fasta file with spliced CDS for each GFF transcript
- -y
- write a protein fasta file with the translation of CDS for each
record
- -W
- for -w and -x options, write in the FASTA defline the exon
coordinates projected onto the spliced sequence; for -y option,
write transcript attributes in the FASTA defline
- -S
- for -y option, use '*' instead of '.' as stop codon
translation
- -L
- Ensembl GTF to GFF3 conversion (implies -F; should be used with
-m)
- -m
- <chr_replace> is a name mapping table for converting reference
sequence names, having this 2-column format: <original_ref_ID>
<new_ref_ID> WARNING: all GFF records on reference sequences whose
original IDs are not found in the 1st column of this table will be
discarded!
- -t
- use <trackname> in the 2nd column of each GFF/GTF output line
- -o
- print the GFF records to <outfile.gff> (those that passed any given
filters). Use -o- to enable printing of to stdout
- -T
- for -o, output will be GTF instead of GFF3
--bed for -o, output BED format instead of
GFF3
--tlf for -o, output "transcript line
format" which is like GFF
- but exons, CDS features and related data are stored as GFF attributes in
the transcript feature line, like this:
- exoncount=N;exons=<exons>;CDSphase=<N>;CDS=<CDScoords>
- <exons> is a comma-delimited list of exon_start-exon_end
coordinates; <CDScoords> is CDS_start:CDS_end coordinates or a list
like <exons>;
-v,-E expose (warn about) duplicate transcript IDs and
other potential
- problems with the given GFF/GTF records
This manpage was written by Andreas Tille for the Debian
distribution and can be used for any other usage of the program.