6.3.3.6. gtf2bed

The gtf2bed script converts 1-based, closed [start, end] Gene Transfer Format v2.2 (GTF2.2) to sorted, 0-based, half-open [start-1, end) extended BED-formatted data.

For convenience, we also offer gtf2starch, which performs the extra step of creating a Starch-formatted archive.

6.3.3.6.1. Dependencies

The gtf2bed script requires convert2bed. The gtf2starch script requires starch. Both dependencies are part of a typical BEDOPS installation.

This script is also dependent on input that follows the GTF 2.2 specification. A GTF-format validator is available here to ensure your input follows specification.

Tip

Conversion of data which are GTF-like, but which do not follow the specification can cause parsing issues. If you run into problems, please check that your input follows the GTF specification.

6.3.3.6.2. Source

The gtf2bed and gtf2starch conversion scripts are part of the binary and source downloads of BEDOPS. See the Installation documentation for more details.

6.3.3.6.3. Usage

The gtf2bed script parses GTF from standard input and prints sorted BED to standard output. The gtf2starch script uses an extra step to parse GTF to a compressed BEDOPS Starch-formatted archive, which is also directed to standard output.

Tip

By default, all conversion scripts now output sorted BED data ready for use with BEDOPS utilities. If you do not want to sort converted output, use the --do-not-sort option. Run the script with the --help option for more details.

Tip

If sorting converted data larger than system memory, use the --max-mem option to limit sort memory usage to a reasonable fraction of available memory, e.g., --max-mem 2G or similar. See --help for more details.

6.3.3.6.4. Example

To demonstrate these scripts, we use a sample GTF input called foo.gtf (see the Downloads section to grab this file).

chr20      protein_coding  exon    9874841 9874841 .       +       .       gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT0000002.4.28"; gene_name "ZNF366";
chr20      protein_coding  CDS     9873504 9874841 .       +       0       gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT0000002.4.28"; gene_name "ZNF366";
chr20      protein_coding  exon    9877488 9877679 .       +       .       gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT0000002.4.28";

We can convert it to sorted BED data in the following manner:

$ gtf2bed < foo.gtf
chr20   9874840 9874841 ZNF366  .       +       protein_coding  exon    .       gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT0000002.4.28"; gene_name "ZNF366"; zero_length_insertion "True";
chr20   9873503 9874841 ZNF366  .       +       protein_coding  CDS     0       gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT0000002.4.28"; gene_name "ZNF366";
chr20   9877487 9877679 ENSBTAG00000020601      .       +       protein_coding  exon    .       gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT0000002.4.28";

Tip

After, say, performing set or statistical operations with bedops, bedmap etc., converting data back to GTF is accomplished through an awk statement that re-orders columns and shifts the coordinate index:

$ awk '{print $1"\t"$7"\t"$8"\t"($2+1)"\t"$3"\t"$5"\t"$6"\t"$9"\t"(substr($0, index($0,$10)))}' foo_subset.bed > foo_subset.gtf

Note

Zero-length insertion elements are given an extra attribute called zero_length_insertion which lets a BED-to-GTF or other parser know that the element will require conversion back to a right-closed element [a, b], where a and b are equal.

Note

Note the conversion from 1- to 0-based coordinate indexing, in the transition from GTF to BED. BEDOPS supports operations on input with any coordinate indexing, but the coordinate change made here is believed to be convenient for most end users.

6.3.3.6.5. Column mapping

In this section, we describe how GTF2.2 columns are mapped to BED columns. We start with the first six UCSC BED columns as follows:

GFF2.2 field BED column index BED field
seqname 1 chromosome
start 2 start
end 3 stop
gene_id 4 id
score 5 score
strand 6 strand

The remaining columns are mapped as follows:

GFF2.2 field BED column index BED field
source 7  
feature 8  
frame 9  
attributes 10  

If present in the GTF2.2 input, the following column is also mapped:

GFF2.2 field BED column index BED field
comments 11  

If we encounter zero-length insertion elements (which are defined where the start and stop GFF3 field values are equivalent), the start coordinate is decremented to convert to 0-based, half-open indexing, and a zero_length_insertion attribute is added to the attributes GTF2.2 field value.

6.3.3.6.6. Downloads