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bedtools

A swiss-army knife of tools for genomic-analysis tasks. Used to intersect, group, convert and count data in BAM, BED, GFF/GTF, VCF format. More information: https://bedtools.readthedocs.io.

Intersect two files regarding the sequences' strand and save the result to the specified file:

bedtools intersect -a {{path/to/file1}} -b {{path/to/file2}} -s > {{path/to/output_file}}

Intersect two files with a left outer join, i.e. report each feature from file1 and NULL if no overlap with file2:

bedtools intersect -a {{path/to/file1}} -b {{path/to/file2}} -lof > {{path/to/output_file}}

Using more efficient algorithm to intersect two pre-sorted files:

bedtools intersect -a {{path/to/file1}} -b {{path/to/file2}} -sorted > {{path/to/output_file}}

Group file path/to/file based on the first three and the fifth column and summarize the sixth column by summing it up:

bedtools groupby -i {{path/to/file}} -c 1-3,5 -g 6 -o sum

Convert bam-formatted file to a bed-formatted one:

bedtools bamtobed -i {{path/to/file.bam}} > {{path/to/file.bed}}

Find for all features in file1.bed the closest one in file2.bed and write their distance in an extra column (input files must be sorted):

bedtools closest -a {{path/to/file1.bed}} -b {{path/to/file2.bed}} -d