bedtools getfasta

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Extract sequences from a FASTA file for each of the intervals defined in a BED/GFF/VCF file.

Category

Genomic Interval Manipulation

Usage

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

Manual

This tool is part of the bedtools suite and it's also known as getFastaFromBed.

Schematic summary of the functionality

Input fasta:     ACAGACTGGTATGAAGGTGGCCACAATTCAGAAAGAAAAAAGAAGAGC
Bed:                ====    =======                 =======
Output fasta:       GACT    TGAAGGT                 AAAAAAG

Required arguments

  • -fi <fasta>: Input FASTA file
  • -bed <bed/gff/vcf>: Bed/Gff/Vcf file that contains intervals you want to retreive their corresponding sequences.

Options

  • -fo <str>: 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

Tips

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

Examples

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
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
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.

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

File formats this tool works with
BEDFASTA

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