5.12 maskFastaFromBed

maskFastaFromBed 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 fro 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.

5.12.1 Usage and option summary

Usage:

maskFastaFromBed [OPTIONS] -fi <input FASTA> -bed <BED/GFF/VCF> -fo <output FASTA>

NOTE: The input and output FASTA files must be different.

Option	Description
-soft	Soft-mask (that is, convert to lower-case bases) the FASTA sequence. By default, hard-masking (that is, conversion to Ns) is performed.

5.12.2 Default behavior

maskFastaFromBed 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.

For example:

cat test.fa
>chr1
AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG

cat test.bed
chr1 5 10

maskFastaFromBed -fi test.fa -bed test.bed -fo test.fa.out

cat test.fa.out
>chr1
AAAAANNNNNCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG

5.12.3 Soft-masking the FASTA file.

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

For example:

cat test.fa
>chr1
AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG

cat test.bed
chr1 5 10

maskFastaFromBed -fi test.fa -bed test.bed -fo test.fa.out -soft

cat test.fa.out
>chr1
AAAAAaaaccCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG