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**annotateBed** annotates one BED/VCF/GFF file with the coverage and number of overlaps observed
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from multiple other BED/VCF/GFF files. In this way, it allows one to ask to what degree one feature
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coincides with multiple other feature types with a single command.
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==========================================================================
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5.24.1 Usage and option summary
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==========================================================================
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annotateBed [OPTIONS] -i <BED/GFF/VCF> -files FILE1 FILE2 FILE3 ... FILEn
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=========================== ===============================================================================================================================================================================================================
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=========================== ===============================================================================================================================================================================================================
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**-namesr** A list of names (one per file) to describe each file in -i. These names will be printed as a header line.
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**-counts** Report the count of features in each file that overlap -i. Default behavior is to report the fraction of -i covered by each file.
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**-both** Report the count of features followed by the % coverage for each annotation file. Default is to report solely the fraction of -i covered by each file.
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**-s** Force strandedness. That is, only include hits in A that overlap B on the same strand. By default, hits are included without respect to strand.
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=========================== ===============================================================================================================================================================================================================
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==========================================================================
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5.24.2 Default behavior - annotate one file with coverage from others.
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==========================================================================
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By default, the fraction of each feature covered by each annotation file is reported after the complete
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feature in the file to be annotated.
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chr1 100 200 nasty 1 -
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chr2 500 1000 ugly 2 +
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chr3 1000 5000 big 3 -
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chr1 150 200 geneA 1 +
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chr1 175 250 geneB 2 +
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chr3 0 10000 geneC 3 -
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chr1 0 10000 cons1 1 +
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chr2 700 10000 cons2 2 -
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chr3 4000 10000 cons3 3 +
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annotateBed -i variants.bed -files genes.bed conserv.bed known_var.bed
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chr1 100 200 nasty 1 - 0.500000 1.000000 0.300000
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chr2 500 1000 ugly 2 + 0.000000 0.600000 1.000000
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chr3 1000 5000 big 3 - 1.000000 0.250000 0.000000
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==========================================================================
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5.24.3 Report the count of hits from the annotation files
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==========================================================================
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annotateBed -counts -i variants.bed -files genes.bed conserv.bed known_var.bed
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chr1 100 200 nasty 1 - 2 1 2
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chr2 500 1000 ugly 2 + 0 1 1
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chr3 1000 5000 big 3 - 1 1 0
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==========================================================================
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5.24.4 Report both the count of hits and the fraction covered from the annotation files
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==========================================================================
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annotateBed -both -i variants.bed -files genes.bed conserv.bed known_var.bed
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#chr start end name score +/- cnt1 pct1 cnt2 pct2 cnt3 pct3
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chr1 100 200 nasty 1 - 2 0.500000 1 1.000000 2 0.300000
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chr2 500 1000 ugly 2 + 0 0.000000 1 0.600000 1 1.000000
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chr3 1000 5000 big 3 - 1 1.000000 1 0.250000 0 0.000000
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==========================================================================
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5.24.5 Restrict the reporting to overlaps on the same strand.
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==========================================================================
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Note: Compare with the result from 5.24.3
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annotateBed -s -i variants.bed -files genes.bed conserv.bed known_var.bed
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chr1 100 200 nasty var1 - 0.000000 0.000000 0.000000
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chr2 500 1000 ugly var2 + 0.000000 0.000000 0.000000
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chr3 1000 5000 big var3 - 1.000000 0.000000 0.000000
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docs/content/annotateBed.rst
