############### 5.24 annotateBed ############### **annotateBed** annotates one BED/VCF/GFF file with the coverage and number of overlaps observed from multiple other BED/VCF/GFF files. In this way, it allows one to ask to what degree one feature coincides with multiple other feature types with a single command. ========================================================================== 5.24.1 Usage and option summary ========================================================================== Usage: :: annotateBed [OPTIONS] -i -files FILE1 FILE2 FILE3 ... FILEn =========================== =============================================================================================================================================================================================================== Option Description =========================== =============================================================================================================================================================================================================== **-namesr** A list of names (one per file) to describe each file in -i. These names will be printed as a header line. **-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. **-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. **-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. =========================== =============================================================================================================================================================================================================== ========================================================================== 5.24.2 Default behavior - annotate one file with coverage from others. ========================================================================== By default, the fraction of each feature covered by each annotation file is reported after the complete feature in the file to be annotated. :: cat variants.bed chr1 100 200 nasty 1 - chr2 500 1000 ugly 2 + chr3 1000 5000 big 3 - cat genes.bed chr1 150 200 geneA 1 + chr1 175 250 geneB 2 + chr3 0 10000 geneC 3 - cat conserve.bed chr1 0 10000 cons1 1 + chr2 700 10000 cons2 2 - chr3 4000 10000 cons3 3 + cat known_var.bed chr1 0 120 known1 - chr1 150 160 known2 - chr2 0 10000 known3 + annotateBed -i variants.bed -files genes.bed conserv.bed known_var.bed chr1 100 200 nasty 1 - 0.500000 1.000000 0.300000 chr2 500 1000 ugly 2 + 0.000000 0.600000 1.000000 chr3 1000 5000 big 3 - 1.000000 0.250000 0.000000 ========================================================================== 5.24.3 Report the count of hits from the annotation files ========================================================================== Figure: :: annotateBed -counts -i variants.bed -files genes.bed conserv.bed known_var.bed chr1 100 200 nasty 1 - 2 1 2 chr2 500 1000 ugly 2 + 0 1 1 chr3 1000 5000 big 3 - 1 1 0 ========================================================================== 5.24.4 Report both the count of hits and the fraction covered from the annotation files ========================================================================== Figure: :: annotateBed -both -i variants.bed -files genes.bed conserv.bed known_var.bed #chr start end name score +/- cnt1 pct1 cnt2 pct2 cnt3 pct3 chr1 100 200 nasty 1 - 2 0.500000 1 1.000000 2 0.300000 chr2 500 1000 ugly 2 + 0 0.000000 1 0.600000 1 1.000000 chr3 1000 5000 big 3 - 1 1.000000 1 0.250000 0 0.000000 ========================================================================== 5.24.5 Restrict the reporting to overlaps on the same strand. ========================================================================== Note: Compare with the result from 5.24.3 :: annotateBed -s -i variants.bed -files genes.bed conserv.bed known_var.bed chr1 100 200 nasty var1 - 0.000000 0.000000 0.000000 chr2 500 1000 ugly var2 + 0.000000 0.000000 0.000000 chr3 1000 5000 big var3 - 1.000000 0.000000 0.000000