bedtools maskfasta

Reference Code backup Executable files

Mask a fasta file based on feature coordinates

Category

Genomic Interval Manipulation

Usage

bedtools maskfasta [OPTIONS] -fi <fasta> -fo <fasta> -bed <bed/gff/vcf>

Manual

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

bedtools maskfasta masks sequences in a FASTA file based on intervals defined in a feature file. The headers in the input FASTA file must exactly match the chromosome column in the feature file. This may be useful for creating your own masked genome file based on custom annotations or for masking all but your target regions when aligning sequence data from a targeted capture experiment.

Required arguments

  • -fi fasta_file: Input FASTA file.
  • -bed bed_file: BED/GFF/VCF file of ranges to mask in the input FASTA.
  • -fo output_fasta: Output FASTA file.

Options

  • -soft: Enforce "soft" masking. Mask with lower-case bases instead of masking with Ns.
  • -mc masking_character: Replace masking character. Use another character instead of masking with Ns.
  • -fullHeader: Use the full fasta header. By default, only the word before the first space or tab is used.

Examples

Default behavior

bedtools maskfasta will mask a FASTA file based on the intervals in a BED file. The newly masked FASTA file is written to the output FASTA file.

$ cat test.fa
>chr1
AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG

$ cat test.bed
chr1 5 10

$ bedtools maskfasta -fi test.fa -bed test.bed -fo test.fa.out

$ cat test.fa.out
>chr1
AAAAANNNNNCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
Soft-masking the FASTA file

Using the -soft option, one can optionally “soft-mask” the FASTA file.

$ cat test.fa
>chr1
AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG

$ cat test.bed
chr1 5 10

$ bedtools maskfasta -fi test.fa -bed test.bed -fo test.fa.out -soft

$ cat test.fa.out
>chr1
AAAAAaaaccCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
Specify a masking character

Using the -mc option, one can optionally choose a masking character to each base that will be masked by the BED file.

$ cat test.fa
>chr1
AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG

$ cat test.bed
chr1 5 10

$ bedtools maskfasta -fi test.fa -bed test.bed -fo test.fa.out -mc X

$ cat test.fa.out
>chr1
AAAAAXXXXXCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG

File formats this tool works with
BEDFASTA

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