--- name: "gffread" section: "1" platform: "linux" package: "gffread" version: "0.12.7-8" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/gffread" --- # gffread(1) GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction ## NAME gffread - GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction ## SYNOPSIS **gffread** \ \[-g \ \| \\]\[-s \\] \[-o \\] \[-t \\] \[-r \[\[\\]\:\]\..\ \[-R\]\] \[-CTVNJMKQAFPGUBHZWTOLE\] \[-w \\] \[-x \\] \[-y \\] \[-i \\] \[--sort-by \\] ## DESCRIPTION - Filter and convert GFF3/GTF2 records, extract corresponding sequences etc. By default (i.e. without **-O**) only process transcripts, ignore other features. - \ is a GFF file, use '-' for stdin ## OPTIONS - **-i** discard transcripts having an intron larger than \ - **-l** discard transcripts shorter than \ bases - **-r** only show transcripts overlapping coordinate range \..\ (on chromosome/contig \, 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 \ and add it as the value for a 'descr' attribute to the GFF record - **-s** \ is a tab-delimited file providing this info for each of the mapped sequences: \ \ \ (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 \ file ### Misc options: - **-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) ### Clustering: **-M**/--merge : cluster the input transcripts into loci, discarding - "duplicated" transcripts (those with the same exact introns and fully contained or equal boundaries) **-d** \ : for **-M** option, write duplication info to file \ **--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) - **-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** \ is a name mapping table for converting reference sequence names, having this 2-column format: \ \ 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 \ in the 2nd column of each GFF/GTF output line - **-o** print the GFF records to \ (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=\;CDSphase=\;CDS=\ - \ is a comma-delimited list of exon\_start-exon\_end coordinates; \ is CDS\_start:CDS\_end coordinates or a list like \; **-v**,-E expose (warn about) duplicate transcript IDs and other potential - problems with the given GFF/GTF records ## AUTHOR This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.