gffread Filters and/or converts GFF3/GTF2 records
The gffread command is documented with the stringtie package.
gffread v0.12.7. Usage:
gffread [-g <genomic_seqs_fasta> | <dir>] [-s <seq_info.fsize>]
[-o <outfile>] [-t <trackname>] [-r [<strand>]<chr>:<start>-<end> [-R]]
[--jmatch <chr>:<start>-<end>] [--no-pseudo]
[-CTVNJMKQAFPGUBHZWTOLE] [-w <exons.fa>] [-x <cds.fa>] [-y <tr_cds.fa>]
[-j ][--ids <IDs.lst> | --nids <IDs.lst>] [--attrs <attr-list>] [-i <maxintron>]
[--stream] [--bed | --gtf | --tlf] [--table <attrlist>] [--sort-by <ref.lst>]
[<input_gff>]
Filter, convert or cluster GFF/GTF/BED records, extract the sequence of
transcripts (exon or CDS) and more.
By default (i.e. without -O) only transcripts are processed, discarding any
other non-transcript features. Default output is a simplified GFF3 with only
the basic attributes.
Options:
--ids discard records/transcripts if their IDs are not listed in <IDs.lst>
--nids discard records/transcripts if their IDs are listed in <IDs.lst>
-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
--jmatch only output transcripts matching the given junction
-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
Misc options:
-F keep all GFF attributes (for non-exon features)
--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)
--attrs <attr-list> only output the GTF/GFF attributes listed in <attr-list>
which is a comma delimited list of attribute names to
--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)
--stream: fast processing of input GFF/BED transcripts as they are received
((no sorting, exons must be grouped by transcript in the input data)
Clustering:
-M/--merge : cluster the input transcripts into loci, discarding
"redundant" 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)
Output options:
--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)
--t-adopt: try to find a parent gene overlapping/containing a transcript
that does not have any explicit gene Parent
-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)
-j output the junctions and the corresponding transcripts
-w write a fasta file with spliced exons for each transcript
--w-add <N> for the -w option, extract additional <N> bases
both upstream and downstream of the transcript boundaries
--w-nocds for -w, disable the output of CDS info in the FASTA file
-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, -x and -y options, write in the FASTA defline all the exon
coordinates projected onto the spliced sequence;
-S for -y option, use '*' instead of '.' as stop codon translation
-L Ensembl GTF to GFF3 conversion, adds version to IDs
-m <chr_replace> is a name mapping table for converting reference
sequence names, having this 2-column format:
<original_ref_ID> <new_ref_ID>
-t use <trackname> in the 2nd column of each GFF/GTF output line
-o write the output records into <outfile> instead of stdout
-T main output will be GTF instead of GFF3
--bed output records in BED format instead of default GFF3
--tlf output "transcript line format" which is like GFF
but with exons and CDS related features 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>
--table output a simple tab delimited format instead of GFF, with columns
having the values of GFF attributes given in <attrlist>; special
pseudo-attributes (prefixed by @) are recognized:
@id, @geneid, @chr, @start, @end, @strand, @numexons, @exons,
@cds, @covlen, @cdslen
If any of -w/-y/-x FASTA output files are enabled, the same fields
(excluding @id) are appended to the definition line of corresponding
FASTA records
-v,-E expose (warn about) duplicate transcript IDs and other potential
problems with the given GFF/GTF records