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Old 09-20-2016, 06:46 PM   #1
lre1234
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Default weird compiling of bedtools

Hi all,
I am updating to the newest version of bedtools (v2.26). Upon compiling the application, I get a weird effect. Essentially, when I go and use the 'coverage' command, I get an output that is similar to using the 'intersect' command. Oddly, when looking at the 'help' in it and a list of the options, it gives me options that are associated to the intersect. it looks like this:

Quote:
Tool: bedtools coverage (aka coverageBed)
Version: v2.26.0
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.
As far as I am aware (and from previous version of the tool) and using the tool, options like '-bed' were not for 'coverage'.

I've tried this on 2 separate computers (my mac, and our servers), as well as re-downloading the program. I even tried going back a few versions to 2.24, and seem to get a similar result. Has anyone ever seen this before? Any thoughts?
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Old 09-21-2016, 01:43 AM   #2
GenoMax
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Default

Please provide the actual error (if you are getting one) or command you used.
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Old 09-21-2016, 04:26 AM   #3
lre1234
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Join Date: Aug 2011
Posts: 106
Default

The command is:

Quote:
./bedtools coverage -a myfile.sorted.bam -b myregions.bed -s
The output looks exactly like what it would be if you use 'intersect' rather than coverage. Also, the usage and options summary has different options than what is here: http://bedtools.readthedocs.io/en/la.../coverage.html

It seems almost like the coverage function has been replaced with intersect. I should note that I have run this command many times before. Also, if I go back to a very old version (v2.10), the function works just fine.
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