mirror of https://github.com/CrimsonTome/tldr.git
30 lines
1.3 KiB
Markdown
30 lines
1.3 KiB
Markdown
# bedtools
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> A swiss-army knife of tools for genomic-analysis tasks.
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> Used to intersect, group, convert and count data in BAM, BED, GFF/GTF, VCF format.
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> More information: <https://bedtools.readthedocs.io>.
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- Intersect file [a] and file(s) [b] regarding the sequences' [s]trand and save the result to a specific file:
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`bedtools intersect -a {{path/to/file_A}} -b {{path/to/file_B1 path/to/file_B2 ...}} -s > {{path/to/output_file}}`
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- Intersect two files with a [l]eft [o]uter [j]oin, i.e. report each feature from `file1` and NULL if no overlap with `file2`:
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`bedtools intersect -a {{path/to/file1}} -b {{path/to/file2}} -loj > {{path/to/output_file}}`
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- Using more efficient algorithm to intersect two pre-sorted files:
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`bedtools intersect -a {{path/to/file1}} -b {{path/to/file2}} -sorted > {{path/to/output_file}}`
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- [g]roup a file based on the first three and the fifth [c]olumn and apply the sum [o]peration on the sixth column:
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`bedtools groupby -i {{path/to/file}} -c 1-3,5 -g 6 -o sum`
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- Convert bam-formatted [i]nput file to a bed-formatted one:
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`bedtools bamtobed -i {{path/to/file.bam}} > {{path/to/file.bed}}`
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- Find for all features in `file1.bed` the closest one in `file2.bed` and write their [d]istance in an extra column (input files must be sorted):
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`bedtools closest -a {{path/to/file1.bed}} -b {{path/to/file2.bed}} -d`
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