bedtools/bedtools_intersect

feature intersection

BAM

BED

GFF

VCF

overlap

Description

Find overlaps between genomic features from two sets of intervals.

bedtools intersect allows one to screen for overlaps between two sets of genomic features.
Moreover, it allows one to have fine control as to how the intersections are reported.
bedtools intersect works with both BED/GFF/VCF and BAM files as input.

Input arguments

Name	Type & Properties	Description
--input_a -a	file required	The input file (BED/GFF/VCF/BAM) to be used as the -a file.
--input_b -b	file required multiple	The input file(s) (BED/GFF/VCF/BAM) to be used as the -b file(s).

Name

Type & Properties

--input_a

-a

file

required

--input_b

-b

file

required

multiple

Output arguments

Name	Type & Properties	Description
--output	file required output	The output BED file.

Name

Type & Properties

--output

file

required

output

Output format options

Name	Type & Properties	Description
--write_a -wa	boolean_true	Write the original A entry for each overlap.
--write_b -wb	boolean_true	Write the original B entry for each overlap. Useful for knowing _what_ A overlaps. Restricted by -f and -r.
--left_outer_join -loj	boolean_true	Perform a "left outer join". That is, for each feature in A report each overlap with B. If no overlaps are found, report a NULL feature for B.
--write_overlap -wo	boolean_true	Write the original A and B entries plus the number of base pairs of overlap between the two features. Overlaps restricted by -f and -r. Only A features with overlap are reported.
--write_overlap_plus -wao	boolean_true	Write the original A and B entries plus the number of base pairs of overlap between the two features. Overlaps restricted by -f and -r. However, A features w/o overlap are also reported with a NULL B feature and overlap = 0.
--report_A_if_no_overlap -u	boolean_true	Write the original A entry _if_ no overlap is found. In other words, just report the fact >=1 hit was found. Overlaps restricted by -f and -r.
--number_of_overlaps_A -c	boolean_true	For each entry in A, report the number of overlaps with B. Reports 0 for A entries that have no overlap with B. Overlaps restricted by -f and -r.
--report_no_overlaps_A -v	boolean_true	Only report those entries in A that have _no overlaps_ with B. Similar to "grep -v" (an homage).
--uncompressed_bam -ubam	boolean_true	Write uncompressed BAM output. Default writes compressed BAM.

Name

Type & Properties

--write_a

-wa

boolean_true

--write_b

-wb

boolean_true

--left_outer_join

-loj

boolean_true

--write_overlap

-wo

boolean_true

--write_overlap_plus

-wao

boolean_true

--report_A_if_no_overlap

-u

boolean_true

--number_of_overlaps_A

-c

boolean_true

--report_no_overlaps_A

-v

boolean_true

--uncompressed_bam

-ubam

boolean_true

Filtering options

Name	Type & Properties	Description
--same_strand -s	boolean_true	Require same strandedness. That is, only report hits in B that overlap A on the _same_ strand. By default, overlaps are reported without respect to strand.
--opposite_strand -S	boolean_true	Require different strandedness. That is, only report hits in B that overlap A on the _opposite_ strand. By default, overlaps are reported without respect to strand.
--min_overlap_A -f	double	Minimum overlap required as a fraction of A. Default is 1E-9 (i.e., 1bp).
--min_overlap_B -F	double	Minimum overlap required as a fraction of B. Default is 1E-9 (i.e., 1bp).
--reciprocal_overlap -r	boolean_true	Require that the fraction overlap be reciprocal for A AND B. - In other words, if -f is 0.90 and -r is used, this requires that B overlap 90% of A and A _also_ overlaps 90% of B.
--either_overlap -e	boolean_true	Require that the minimum fraction be satisfied for A OR B. - In other words, if -e is used with -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of B is covered. Without -e, both fractions would have to be satisfied.
--split	boolean_true	Treat "split" BAM or BED12 entries as distinct BED intervals.
--genome -g	file	Provide a genome file to enforce consistent chromosome sort order across input files. Only applies when used with -sorted option.
--nonamecheck	boolean_true	For sorted data, don't throw an error if the file has different naming conventions for the same chromosome (e.g., "chr1" vs "chr01").
--sorted	boolean_true	Use the "chromsweep" algorithm for sorted (-k1,1 -k2,2n) input.
--names	string	When using multiple databases, provide an alias for each that will appear instead of a fileId when also printing the DB record.
--filenames	boolean_true	When using multiple databases, show each complete filename instead of a fileId when also printing the DB record.
--sortout	boolean_true	When using multiple databases, sort the output DB hits for each record.
--bed	boolean_true	If using BAM input, write output as BED.
--header	boolean_true	Print the header from the A file prior to results.
--no_buffer_output --nobuf	boolean_true	Disable buffered output. Using this option will cause each line of output to be printed as it is generated, rather than saved in a buffer. This will make printing large output files noticeably slower, but can be useful in conjunction with other software tools and scripts that need to process one line of bedtools output at a time.
--io_buffer_size --iobuf	integer	Specify amount of memory to use for input buffer. Takes an integer argument. Optional suffixes K/M/G supported. Note: currently has no effect with compressed files.

Name

Type & Properties

--same_strand

-s

boolean_true

--opposite_strand

-S

boolean_true

--min_overlap_A

-f

double

--min_overlap_B

-F

double

--reciprocal_overlap

-r

boolean_true

--either_overlap

-e

boolean_true

--split

boolean_true

--genome

-g

file

--nonamecheck

boolean_true

--sorted

boolean_true

--names

string

--filenames

boolean_true

--sortout

boolean_true

--bed

boolean_true

--header

boolean_true

--no_buffer_output

--nobuf

boolean_true

--io_buffer_size

--iobuf

integer

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.2 \  
  -main-script target/nextflow/bedtools/bedtools_intersect/main.nf \  
  -params-file params.yaml

bedtools/bedtools_intersect

Input arguments

Output arguments

Output format options

Filtering options

Run this component

Relationships

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Uses