Genome Annotation

genePredToGtf
Function: Convert genePred table or file to gtf.
Usage: genePredToGtf database genePredTable output.gtf
GffCompare
Function: Compare, merge, annotate and estimate accuracy of one or more GFF files (the “query” files), when compared with a reference annotation (also provided as GFF).
Usage: gffcompare [options]* {-i <input_gtf_list> | <input1.gtf> [<input2.gtf> .. <inputN.gtf>]}
StringTie
Function: This is a special usage mode of StringTie, distinct from the assembly usage mode. In the merge mode, StringTie takes as input a list of GTF/GFF files and merges/assembles these transcripts into a non-redundant set of transcripts. This mode is used in the new differential analysis pipeline to generate a global, unified set of transcripts (isoforms) across multiple RNA-Seq samples. If a reference annotation is provided, StringTie will assemble the transfrags from the input GTF files with the reference transcripts.
Usage: stringtie <aligned_reads.bam> [options]*
GEMINI annotate
Function: It is inevitable that researchers will want to enhance the GEMINI framework with their own, custom annotations. GEMINI provides a sub-command called annotate for exactly this purpose.
Usage: gemini load -v my.vcf -t snpEff my.db
AnnotateTable.py
Function: AnnotateTable.py annotates individual positions of a table file according to annotations indexed by tabix tool. It adds from 1 to 3 additional columns according to -c option.
Usage: AnnotateTable.py -i mytable -a rmsk.gtf.gz -u -c1,2,3 -n rmsk -o mytable_rmsk
GeneTrack
Function: GeneTrack separately identifies peaks on the forward "+” (W) and reverse “-” (C) strand.
Usage: genetrack.py [options] input_paths
pints_caller
Function: Identify transcriptional regulatory elements (enhancers and promoters) from sequencing libraries of transcription start site assays
Usage: pints_caller --file-prefix FILE_PREFIX --bam-file [BAM_FILE ...] [--exp-type GROcap,etc.]
pints_caller
Function: Identify transcriptional regulatory elements (enhancers and promoters) from sequencing libraries of transcription start site assays
Usage: pints_caller --file-prefix FILE_PREFIX --bw-pl [BW_PL ...] --bw-mn [BW_MN ...]