Bedtools

bedtools : a powerful toolset for genome arithmetic

https://bedtools.readthedocs.io/en/latest/

Souce code : https://github.com/arq5x/bedtools2

Install

https://github.com/arq5x/bedtools2/releases

Download binary file

$ wget https://github.com/arq5x/bedtools2/releases/download/v2.29.2/bedtools.static.binary
$ mv bedtools.static.binary bedtools
$ chmod a+x bedtools

getfasta

https://bedtools.readthedocs.io/en/latest/_images/getfasta-glyph.png

$ bedtools getfasta -fi hg38.fa -bed Exome.bed -fo hg38_bed.fa
$ cat hg38_bed.fa
>1:12080-12251
GAGAGGAGCCATGCCTAGAGTGGGATGGGCCATTGTTCATCTTCTGGCCCCTGTTGTCTGCATGTAACTTAATACCACAACCAGGCATAGGGGAAAGATTGGAGGAAAGATGAGTGAGAGCATCAACTTCTCTCACAACCTAGGCCAGTAAGTAGTGCTTGTGCTCATCTC
>1:12595-12802
CTCCTGTCTCCCCCCAGGTGTGTGGTGATGCCAGGCATGCCCTTCCCCAGCATCAGGTCTCCAGAGCTGCAGAAGACGACGGCCGACTTGGATCACACTCTTGTGAGTGTCCCCAGTGTTGCAGAGGTGAGAGGAGAGTAGACAGTGAGTGGGAGTGGCGTCGCCCCTAGGGCTCTACGGGGCCGGCG
...

https://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html

Merge

bedtools merge combines overlapping or “book-ended” features in an interval file into a single feature which spans all of the combined features.

https://bedtools.readthedocs.io/en/latest/content/tools/merge.html

Bed files : https://github.com/AstraZeneca-NGS/reference_data/tree/master/hg38/bed

$ less data.bed
chr1    13259210        13259717        PRAMEF5
chr1    13259262        13259307        PRAMEF5
chr1    13259547        13259624        PRAMEF5

$ bedtools merge -i data.bed -c 4 -o collapse
chr1    13259210        13259717        PRAMEF5,PRAMEF5,PRAMEF5

$ bedtools merge -i data.bed -c 4 -o distinct
chr1    13259210        13259717        PRAMEF5

$ bedtools merge -i data.bed -header
chr1    13259210        13259717