---
title: "bedtools-cov"
output: html_document
---

Tool:    bedtools coverage (aka coverageBed)
Version: v2.30.0
Summary: Returns the depth and breadth of coverage of features from B
	 on the intervals in A.

Usage:   bedtools coverage [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>

Options: 
	-hist	Report a histogram of coverage for each feature in A
		as well as a summary histogram for _all_ features in A.

		Output (tab delimited) after each feature in A:
		  1) depth
		  2) # bases at depth
		  3) size of A
		  4) % of A at depth

	-d	Report the depth at each position in each A feature.
		Positions reported are one based.  Each position
		and depth follow the complete A feature.

	-counts	Only report the count of overlaps, don't compute fraction, etc.

	-mean	Report the mean depth of all positions in each A feature.

	-s	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.

	-S	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.

	-f	Minimum overlap required as a fraction of A.
		- Default is 1E-9 (i.e., 1bp).
		- FLOAT (e.g. 0.50)

	-F	Minimum overlap required as a fraction of B.
		- Default is 1E-9 (i.e., 1bp).
		- FLOAT (e.g. 0.50)

	-r	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.

	-e	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	Treat "split" BAM or BED12 entries as distinct BED intervals.

	-g	Provide a genome file to enforce consistent chromosome sort order
		across input files. Only applies when used with -sorted option.

	-nonamecheck	For sorted data, don't throw an error if the file has different naming conventions
			for the same chromosome. ex. "chr1" vs "chr01".

	-sorted	Use the "chromsweep" algorithm for sorted (-k1,1 -k2,2n) input.

	-bed	If using BAM input, write output as BED.

	-header	Print the header from the A file prior to results.

	-nobuf	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.

	-iobuf	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.

Default Output:  
	 After each entry in A, reports: 
	   1) The number of features in B that overlapped the A interval.
	   2) The number of bases in A that had non-zero coverage.
	   3) The length of the entry in A.
	   4) The fraction of bases in A that had non-zero coverage.




```{bash}
/home/shared/bedtools2/bin/bedtools coverage \
-a ../data/busco-single-copy.bed \
-b ../analyses/SRR12227929.bam \
> ../analyses/cov.out

```

```{bash}
/home/shared/bedtools2/bin/bedtools coverage \
-hist \
-a ../data/busco-single-copy.bed \
-b ../analyses/SRR12227929.bam \
> ../analyses/cov_h.out

```

```{bash}
/home/shared/bedtools2/bin/bedtools coverage \
-mean \
-a ../data/busco-single-copy.bed \
-b ../analyses/SRR12227929.bam \
> ../analyses/cov_m.out

```



```{bash}
/usr/bin/wget -r \
--no-check-certificate \
--quiet \
--no-directories --no-parent \
-P ../bg_data/ \
-A *sorted.bam \
https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/071521-cvBS/
```



```{bash}
/home/shared/bedtools2/bin/bedtools coverage \
-mean \
-a ../data/C_virginica-3.0_Gnomon_genes.bed  \
-b /home/sr320/github/2018_L18-adult-methylation/bg_data/9M_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam \
> ../analyses/9M_cov_m.out
```





