Hi all,
I just posted the latest version of BEDTools (Version 2.8). The main highlights of this release are 1) native support for VCF (v4.0), 2) proper support for both split BAM alignments and blocked BED features, 3) a new and very useful tool called groupBy, 4) a new tool called bed12ToBed6, and several bug fixes. The gory details are below.
Expect some additional minor releases with further updates this summer.
Cheers,
Aaron
Download: http://bedtools.googlecode.com/files....v2.8.0.tar.gz
Detailed release notes:
1. Proper support for "split" BAM alignments and "blocked" BED (aka BED12) features. By using the "-split" option, intersectBed, coverageBed, genomeCoverageBed, and bamToBed will now correctly compute overlaps/coverage solely for the "split" portions of BAM alignments or the "blocks" of BED12 features such as genes.
2. Added native support for the 1000 Genome Variant Calling Format (VCF) version 4.0.
3. New bed12ToBed6 tool. This tool will convert each block of a BED12 feature into discrete BED6 features.
4. Useful new groupBy tool. This new tool mimics the "groupBy" clause in SQL. Given a file or stream that is sorted by the appropriate "grouping columns", groupBy will compute summary statistics on another column in the file or stream. This will work with output from all BEDTools as well as any other tab-delimited file or stream. Example summary operations include: sum, mean, stdev, min, max, etc. Please see the help for the tools for examples.
5. Improvements to genomeCoverageBed. Most notably, beyond the several efficiency and organizational changes made, it now includes a "-strand" option which allows one to specify that coverage should only be computed on either the "+" or the "-" strand.
6. Fixed a bug in closestBed which incorrectly reported "null" overlaps for features that did not have a closest feature in the B file.
7. Fixed a careless bug in slopBed that caused an infinite loop when the "-excl" option was used.
8. Reduced memory consumption by ca. 15% and run time by ca. 10% for most tools.
9. Several code-cleanliness updates such as templated functions and common tyedefs.
10. Tweaked the genome binning approach such that 16kb bins are the most granular.
I just posted the latest version of BEDTools (Version 2.8). The main highlights of this release are 1) native support for VCF (v4.0), 2) proper support for both split BAM alignments and blocked BED features, 3) a new and very useful tool called groupBy, 4) a new tool called bed12ToBed6, and several bug fixes. The gory details are below.
Expect some additional minor releases with further updates this summer.
Cheers,
Aaron
Download: http://bedtools.googlecode.com/files....v2.8.0.tar.gz
Detailed release notes:
1. Proper support for "split" BAM alignments and "blocked" BED (aka BED12) features. By using the "-split" option, intersectBed, coverageBed, genomeCoverageBed, and bamToBed will now correctly compute overlaps/coverage solely for the "split" portions of BAM alignments or the "blocks" of BED12 features such as genes.
2. Added native support for the 1000 Genome Variant Calling Format (VCF) version 4.0.
3. New bed12ToBed6 tool. This tool will convert each block of a BED12 feature into discrete BED6 features.
4. Useful new groupBy tool. This new tool mimics the "groupBy" clause in SQL. Given a file or stream that is sorted by the appropriate "grouping columns", groupBy will compute summary statistics on another column in the file or stream. This will work with output from all BEDTools as well as any other tab-delimited file or stream. Example summary operations include: sum, mean, stdev, min, max, etc. Please see the help for the tools for examples.
5. Improvements to genomeCoverageBed. Most notably, beyond the several efficiency and organizational changes made, it now includes a "-strand" option which allows one to specify that coverage should only be computed on either the "+" or the "-" strand.
6. Fixed a bug in closestBed which incorrectly reported "null" overlaps for features that did not have a closest feature in the B file.
7. Fixed a careless bug in slopBed that caused an infinite loop when the "-excl" option was used.
8. Reduced memory consumption by ca. 15% and run time by ca. 10% for most tools.
9. Several code-cleanliness updates such as templated functions and common tyedefs.
10. Tweaked the genome binning approach such that 16kb bins are the most granular.
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