getfasta — bedtools 2.31.0 documentation

# getfasta

`bedtools getfasta` extracts sequences from a FASTA file for each of the intervals defined in a BED/GFF/VCF file.

Tip

1. The headers in the input FASTA file must exactly match the chromosome column in the BED file.

2. You can use the UNIX `fold` command to set the line width of the FASTA output. For example, `fold -w 60` will make each line of the FASTA file have at most 60 nucleotides for easy viewing.

3. BED files containing a single region require a newline character at the end of the line, otherwise a blank output file is produced.

See also

maskfasta

## Usage and option summary

Usage

    $ bedtools getfasta [OPTIONS] -fi <input FASTA> -bed <BED/GFF/VCF>

(or):

    $ getFastaFromBed [OPTIONS] -fi <input FASTA> -bed <BED/GFF/VCF>

Option | Description
--- | ---
-fo | Specify an output file name. By default, output goes to stdout.
-name | Use the name field and coordinates for the FASTA header
-name+ | (deprecated) Use the name field and coordinates for the FASTA header
-nameOnly | Use the name field for the FASTA header
-tab | Report extract sequences in a tab-delimited format instead of in FASTA format.
-bedOut | Report extract sequences in a tab-delimited BED format instead of in FASTA format.
-s | Force strandedness. If the feature occupies the antisense strand, the sequence will be reverse complemented. Default: strand information is ignored.
-split | Given BED12 input, extract and concatenate the sequences from the BED “blocks” (e.g., exons)
-fullHeader | Use full fasta header. By default, only the word before the first space or tab is used.
-rna | The FASTA is RNA not DNA. Reverse complementation handled accordingly.

## Default behavior

`bedtools getfasta` will extract the sequence defined by the coordinates in a BED interval and create a new FASTA entry in the output file for each extracted sequence. By default, the FASTA header for each extracted sequence will be formatted as follows: “<chrom>:<start>-<end>”.

    $ cat test.fa
    >chr1
    AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG

    $ cat test.bed
    chr1 5 10

    $ bedtools getfasta -fi test.fa -bed test.bed
    >chr1:5-10
    AAACC

    # optionally write to an output file
    $ bedtools getfasta -fi test.fa -bed test.bed -fo test.fa.out

    $ cat test.fa.out
    >chr1:5-10
    AAACC

## `-name` Using the BED “name” column as a FASTA header.

Using the `-name` option, one can set the FASTA header for each extracted sequence to be the “name” columns from the BED feature.

    $ cat test.fa
    >chr1
    AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG

    $ cat test.bed
    chr1 5 10 myseq

    $ bedtools getfasta -fi test.fa -bed test.bed -name
    >myseq
    AAACC

## `-tab` Creating a tab-delimited output file in lieu of FASTA output.

Using the `-tab` option, the `-fo` output file will be tab-delimited instead of in FASTA format.

    $ cat test.fa
    >chr1
    AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG

    $ cat test.bed
    chr1 5 10 myseq

    $ bedtools getfasta -fi test.fa -bed test.bed -name -tab
    myseq AAACC

## `-bedOut` Creating a tab-delimited BED file in lieu of FASTA output.

Using the `-tab` option, the `-fo` output file will be tab-delimited instead of in FASTA format.

    $ cat test.fa
    >chr1
    AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG

    $ cat test.bed
    chr1 5 10 myseq

    $ bedtools getfasta -fi test.fa -bed test.bed -tab
    chr1 5 10 AAACC

## `-s` Forcing the extracted sequence to reflect the requested strand

`bedtools getfasta` will extract the sequence in the orientation defined in the strand column when the “-s” option is used.

    $ cat test.fa
    >chr1
    AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG

    $ cat test.bed
    chr1 20 25 forward 1 +
    chr1 20 25 reverse 1 -

    $ bedtools getfasta -fi test.fa -bed test.bed -s -name
    >forward
    CGCTA
    >reverse
    TAGCG

## `-split` Extracting BED “blocks”.

One can optionally request that FASTA records be extracting and concatenating each block in a BED12 record. For example, consider a BED12 record describing a transcript. By default, `getfasta` will extract the sequence representing the entire transcript (introns, exons, UTRs). Using the -split option, `getfasta` will instead produce separate a FASTA record representing a transcript that splices together each BED12 block (e.g., exons and UTRs in the case of genes described with BED12).

    $ cat genes.bed12
    chr1  164404  173864  ENST00000466557.1       0       -       173864  173864  0       6       387,59,66,216,132,112,  0,1479,3695,4644,8152,9348,
    chr1  235855  267253  ENST00000424587.1       0       -       267253  267253  0       4       2100,150,105,158,       0,2562,23161,31240,
    chr1  317810  328455  ENST00000426316.1       0       +       328455  328455  0       2       323,145,        0,10500,

    $ bedtools getfasta -fi chr1.fa -bed genes.bed12 -split -name
    >ENST00000466557.1
    gaggcgggaagatcacttgatatcaggagtcgaggcgggaagatcacttgacgtcaggagttcgagactggcccggccaacatggtgaaaccgcatctccactaaaaatacaaaaattagcctggtatggtggtgggcacctgtaatcccagtgacttgggaggctaaggcaggagaatttcttgaacccaggaggcagaggttgcagtgaccagcaaggttgcgccattgcaccccagcctgggcgataagagtgaaaactccatctcaaaaaaaaaaaaaaaaaaaaaaTTCCTTTGGGAAGGCCTTCTACATAAAAATCTTCAACATGAGACTGGAAAAAAGGGTATGGGATCATCACCGGACCTTTGGCTTTTACAGCTCGAGCTGACAAAGTTGATTTATCAAGTTGTAAATCTTCACCTGTTGAATTCATAAGTTCATGTCATATTTTCTTTCAGACAATTCTTCAGTTTGTTTACGTAGATCAGCGATACGATGATTCCATTTCTtcggatccttgtaagagcagagcaggtgatggagagggtgggaggtgtagtgacagaagcaggaaactccagtcattcgagacgggcagcacaagctgcggagtgcaggccacctctacggccaggaaacggattctcccgcagagcctcggaagctaccgaccctgctcccaccttgactcagtaggacttactgtagaattctggccttcagacCTGAGCCTGGCAGCTCTCTCCAACTTTGGAAGCCCAGGGGCATGGCCCCTGTCCACAGATGCACCTGGCATGAGGCGTGCCCAGAGGGACAGAGGCAGATGAGTttcgtctcctccactggattgtgagggcCAGAGTTGAACTCCCTCATTTTCCGTTCCCCAGCATTGGCAGGTTCTGGGACTGGTGGCTGTGGTGGCTCGTTGGTCTTTGTCTCTTAGAAGGTGGGGAATAATCATCATCT
    >ENST00000424587.1
    ccaggaagtgaaaatgacactttactgttttaatttgcatttctctgcttacaagtggattacacacattttcgtgtgctgttggctacttatTCATTCAGAAAACATACTAAGTGCTGGCTCTTTTTCATGTCCTTTATCAAGTTTGGATCATGTCATTTGCTATTTTCTTTCTGATGTAAACTCTCAAAGTCTGAAGTGTATTGTCTTTTCCTGACACATATGTTGTAAATAATTTTCTGGCTTACATTTTGACTTTTAATTTCATTCACGATGTTTTTAATGAATAATTTTAATTTTTATGAATGCAAGTTAAAATAATTCTTTCATTGTGGTCTCTGACATGTCATGCCAATAAGGGTCTTCTCCTCCAAGAGCACAGAAATATTTGCCAATACTGTCCTTAAAATCGGTCACAGTTTCATTTTTTATATATGCATTTTACTTCAATTGGGGCTTCATTTTACTGAATGCCCTATTTGAAGCAAGTTTCTCAGTTAATTCTTTTCTCAAAGGGCTAAGTATGGTAGATTGCAAACATAAGTGGCCACATAATGCTCTCACCTCctttgcctcctctcccaggaggagatagcgtccatctttccactccttaatctgggcttggccgtgtgacttgcactggccaatgggatattaacaagtctgatgtgcacagaggctgtagaatgtgcacgggggcttggtctctcttgctgccctggagaccagctgccCCACGAAGGAACCAGAGCCAACCTGCTGCTTCCTGGAGGAAGACAGTCCCTCTGTCCCTCTGTCTCTGCCAACCAGTTAACCTGCTGCTTCCTGGAGGGAGACAGTCCCTCAGTCCCTCTGTCTCTGCCAACCAGTTAACCTGCTGCTTCCTGGAGGAAGACAGTCACTCTGTCTCTGccaacccagttgaccgcagacatgcaggtctgctcaggtaagaccagcacagtccctgccctgtgagccaaaccaaatggtccagccacagaatcgtgagcaaataagtgatgcttaagtcactaagatttgggCAAAAGCTGAGCATTTATCCCAATCCCAATACTGTTTGTCCTTCTGTTTATCTGTCTGTCCTTCCCTGCTCATTTAAAATGCCCCCACTGCATCTAGTACATTTTTATAGGATCAGGGATCTGCTCTTGGATTAATGTTGTGTTCCCACCTCGAGGCAGCTTTGTAAGCTTCTGAGCACTTCCCAATTCCGGGTGACTTCAGGCACTGGGAGGCCTGTGCATCAGCTGCTGCTGTCTGTAGCTGACTTCCTTCACCCCTCTGCTGTCCTCAGCTCCTTCACCCCTGGGCCTCAGGAAATCAATGTCATGCTGACATCACTCTAGATCTAAAAGTTGGGTTCTTGgaccaggcgtggtggctcacacctgtaatcccagcactttgggaggccgaggcgggtggatcacaaggtcaggagatcaagacgattctggctaacacggtgaaaccccgtctctactaaaaatacaaaaaaattagccgggtgtggtggcaggtgcctgtagccccagctacttgggaggctgaggcaggagaatggcttgaacctgggaggtggagcttgcagtgagccaagatcacgccactgcactccagaatgggagagagagcgagactttctcaaaaaaaaaaaaaaaaCTTAGGTTCTTGGATGTTCGGGAAAGGGGGTTATTATCTAGGATCCTTGAAGCACCCCCAAGGGCATCTTCTCAAAGTTGGATGTGTGCATTTTCCTGAGAGGAAAGCTTTCCCACATTATACAGCTTCTGAAAGGGTTGCTTGACCCACAGATGTGAAGCTGAGGCTGAAGGAGACTGATGTGGTTTCTCCTCAGTTTCTCTGTGCAGCACCAGGTGGCAGCAGAGGTCAGCAAGGCAAACCCGAGCCCGGGGATGCGGAGTGGGGGCAGCTACGTCCTCTCTTGAGCTACAGCAGATTCACTCTGTTCTGTTTCATTGTTGTTTAGTTTGCGTTGTGTTTCTCCAACTTTGTGCCTCATCAGGAAAAGCTTTGGATCACAATTCCCAGtgctgaagaaaaggccaaactcttggttgtgttctttgattAGTgcctgtgacgcagcttcaggaggtcctgagaacgtgtgcacagtttagtcggcagaaacttagggaaatgtaagaccaccatcagcacataggagttctgcattggtttggtctgcattggtttggtCTTTTCCTGGATACAGGTCTTGATAGGTCTCTTGATGTCATTTCACTTCAGATTCTTCTTTAGAAAACTTGGACAATAGCATTTGCTGTCTTGTCCAAATTGTTACTTCAAGTTTGCTCTTAGCAAGTAATTGTTTCAGTATCTATATCAAAAATGGCTTAAGCCTGCAACATGTTTCTGAATGATTAACAAGGTGATAGTCAGTTCTTCATTGAATCCTGGATGCTTTATTTTTCTTAATAAGAGGAATTCATATGGATCAG
    >ENST00000426316.1
    AATGATCAAATTATGTTTCCCATGCATCAGGTGCAATGGGAAGCTCTTctggagagtgagagaagcttccagttaaggtgacattgaagccaagtcctgaaagatgaggaagagttgtatgagagtggggagggaagggggaggtggagggaTGGGGAATGGGCCGGGATGGGATAGCGCAAACTGCCCGGGAAGGGAAACCAGCACTGTACAGACCTGAACAACGAAGATGGCATATTTTGTTCAGGGAATGGTGAATTAAGTGTGGCAGGAATGCTTTGTAGACACAGTAATTTGCTTGTATGGAATTTTGCCTGAGAGACCTCATTCCTCACGTCGGCCATTCCAGGCCCCGTTTTTCCCTTCCGGCAGCCTCTTGGCCTCTAATTTGTTTATCTTTTGTGTATAAATCCCAAAATATTGAATTTTGGAATATTTCCACCATTATGTAAATATTTTGATAGGTAA

    # use the UNIX fold command to wrap the FASTA sequence such that each line
    # has at most 60 characters
    $ bedtools getfasta -fi chr1.fa -bed genes.bed12 -split -name | \
          fold -w 60
    >ENST00000466557.1
    gaggcgggaagatcacttgatatcaggagtcgaggcgggaagatcacttgacgtcaggag
    ttcgagactggcccggccaacatggtgaaaccgcatctccactaaaaatacaaaaattag
    cctggtatggtggtgggcacctgtaatcccagtgacttgggaggctaaggcaggagaatt
    tcttgaacccaggaggcagaggttgcagtgaccagcaaggttgcgccattgcaccccagc
    ctgggcgataagagtgaaaactccatctcaaaaaaaaaaaaaaaaaaaaaaTTCCTTTGG
    GAAGGCCTTCTACATAAAAATCTTCAACATGAGACTGGAAAAAAGGGTATGGGATCATCA
    CCGGACCTTTGGCTTTTACAGCTCGAGCTGACAAAGTTGATTTATCAAGTTGTAAATCTT
    CACCTGTTGAATTCATAAGTTCATGTCATATTTTCTTTCAGACAATTCTTCAGTTTGTTT
    ACGTAGATCAGCGATACGATGATTCCATTTCTtcggatccttgtaagagcagagcaggtg
    atggagagggtgggaggtgtagtgacagaagcaggaaactccagtcattcgagacgggca
    gcacaagctgcggagtgcaggccacctctacggccaggaaacggattctcccgcagagcc
    tcggaagctaccgaccctgctcccaccttgactcagtaggacttactgtagaattctggc
    cttcagacCTGAGCCTGGCAGCTCTCTCCAACTTTGGAAGCCCAGGGGCATGGCCCCTGT
    CCACAGATGCACCTGGCATGAGGCGTGCCCAGAGGGACAGAGGCAGATGAGTttcgtctc
    ctccactggattgtgagggcCAGAGTTGAACTCCCTCATTTTCCGTTCCCCAGCATTGGC
    AGGTTCTGGGACTGGTGGCTGTGGTGGCTCGTTGGTCTTTGTCTCTTAGAAGGTGGGGAA
    TAATCATCATCT
    >ENST00000424587.1
    ccaggaagtgaaaatgacactttactgttttaatttgcatttctctgcttacaagtggat
    tacacacattttcgtgtgctgttggctacttatTCATTCAGAAAACATACTAAGTGCTGG
    CTCTTTTTCATGTCCTTTATCAAGTTTGGATCATGTCATTTGCTATTTTCTTTCTGATGT
    AAACTCTCAAAGTCTGAAGTGTATTGTCTTTTCCTGACACATATGTTGTAAATAATTTTC
    TGGCTTACATTTTGACTTTTAATTTCATTCACGATGTTTTTAATGAATAATTTTAATTTT
    TATGAATGCAAGTTAAAATAATTCTTTCATTGTGGTCTCTGACATGTCATGCCAATAAGG
    GTCTTCTCCTCCAAGAGCACAGAAATATTTGCCAATACTGTCCTTAAAATCGGTCACAGT
    TTCATTTTTTATATATGCATTTTACTTCAATTGGGGCTTCATTTTACTGAATGCCCTATT
    TGAAGCAAGTTTCTCAGTTAATTCTTTTCTCAAAGGGCTAAGTATGGTAGATTGCAAACA
    TAAGTGGCCACATAATGCTCTCACCTCctttgcctcctctcccaggaggagatagcgtcc
    atctttccactccttaatctgggcttggccgtgtgacttgcactggccaatgggatatta
    acaagtctgatgtgcacagaggctgtagaatgtgcacgggggcttggtctctcttgctgc
    cctggagaccagctgccCCACGAAGGAACCAGAGCCAACCTGCTGCTTCCTGGAGGAAGA
    CAGTCCCTCTGTCCCTCTGTCTCTGCCAACCAGTTAACCTGCTGCTTCCTGGAGGGAGAC
    AGTCCCTCAGTCCCTCTGTCTCTGCCAACCAGTTAACCTGCTGCTTCCTGGAGGAAGACA
    GTCACTCTGTCTCTGccaacccagttgaccgcagacatgcaggtctgctcaggtaagacc
    agcacagtccctgccctgtgagccaaaccaaatggtccagccacagaatcgtgagcaaat
    aagtgatgcttaagtcactaagatttgggCAAAAGCTGAGCATTTATCCCAATCCCAATA
    CTGTTTGTCCTTCTGTTTATCTGTCTGTCCTTCCCTGCTCATTTAAAATGCCCCCACTGC
    ATCTAGTACATTTTTATAGGATCAGGGATCTGCTCTTGGATTAATGTTGTGTTCCCACCT
    CGAGGCAGCTTTGTAAGCTTCTGAGCACTTCCCAATTCCGGGTGACTTCAGGCACTGGGA
    GGCCTGTGCATCAGCTGCTGCTGTCTGTAGCTGACTTCCTTCACCCCTCTGCTGTCCTCA
    GCTCCTTCACCCCTGGGCCTCAGGAAATCAATGTCATGCTGACATCACTCTAGATCTAAA
    AGTTGGGTTCTTGgaccaggcgtggtggctcacacctgtaatcccagcactttgggaggc
    cgaggcgggtggatcacaaggtcaggagatcaagacgattctggctaacacggtgaaacc
    ccgtctctactaaaaatacaaaaaaattagccgggtgtggtggcaggtgcctgtagcccc
    agctacttgggaggctgaggcaggagaatggcttgaacctgggaggtggagcttgcagtg
    agccaagatcacgccactgcactccagaatgggagagagagcgagactttctcaaaaaaa
    aaaaaaaaaCTTAGGTTCTTGGATGTTCGGGAAAGGGGGTTATTATCTAGGATCCTTGAA
    GCACCCCCAAGGGCATCTTCTCAAAGTTGGATGTGTGCATTTTCCTGAGAGGAAAGCTTT
    CCCACATTATACAGCTTCTGAAAGGGTTGCTTGACCCACAGATGTGAAGCTGAGGCTGAA
    GGAGACTGATGTGGTTTCTCCTCAGTTTCTCTGTGCAGCACCAGGTGGCAGCAGAGGTCA
    GCAAGGCAAACCCGAGCCCGGGGATGCGGAGTGGGGGCAGCTACGTCCTCTCTTGAGCTA
    CAGCAGATTCACTCTGTTCTGTTTCATTGTTGTTTAGTTTGCGTTGTGTTTCTCCAACTT
    TGTGCCTCATCAGGAAAAGCTTTGGATCACAATTCCCAGtgctgaagaaaaggccaaact
    cttggttgtgttctttgattAGTgcctgtgacgcagcttcaggaggtcctgagaacgtgt
    gcacagtttagtcggcagaaacttagggaaatgtaagaccaccatcagcacataggagtt
    ctgcattggtttggtctgcattggtttggtCTTTTCCTGGATACAGGTCTTGATAGGTCT
    CTTGATGTCATTTCACTTCAGATTCTTCTTTAGAAAACTTGGACAATAGCATTTGCTGTC
    TTGTCCAAATTGTTACTTCAAGTTTGCTCTTAGCAAGTAATTGTTTCAGTATCTATATCA
    AAAATGGCTTAAGCCTGCAACATGTTTCTGAATGATTAACAAGGTGATAGTCAGTTCTTC
    ATTGAATCCTGGATGCTTTATTTTTCTTAATAAGAGGAATTCATATGGATCAG
    >ENST00000426316.1
    AATGATCAAATTATGTTTCCCATGCATCAGGTGCAATGGGAAGCTCTTctggagagtgag
    agaagcttccagttaaggtgacattgaagccaagtcctgaaagatgaggaagagttgtat
    gagagtggggagggaagggggaggtggagggaTGGGGAATGGGCCGGGATGGGATAGCGC
    AAACTGCCCGGGAAGGGAAACCAGCACTGTACAGACCTGAACAACGAAGATGGCATATTT
    TGTTCAGGGAATGGTGAATTAAGTGTGGCAGGAATGCTTTGTAGACACAGTAATTTGCTT
    GTATGGAATTTTGCCTGAGAGACCTCATTCCTCACGTCGGCCATTCCAGGCCCCGTTTTT
    CCCTTCCGGCAGCCTCTTGGCCTCTAATTTGTTTATCTTTTGTGTATAAATCCCAAAATA
    TTGAATTTTGGAATATTTCCACCATTATGTAAATATTTTGATAGGTAA

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