Variant Analysis

Usage -i rnaseq.bam -f reference.fa -l



-i      BAM file

-I      Sort input BAM file

-f      Reference in fasta file

-l      List of known RNA editing events

-C      Base interval to explore [100000]

-k      List of chromosomes to skip separated by comma or file

-t      Number of threads [1]

-o      Output folder [rediFolder_XXXX] in which all results will be stored. XXXX is a random number generated at each run.

-F      Internal folder name [null] is the main folder containing output tables.

-c      Min. read coverage [10]

-Q      Fastq offset value [33]

-q      Minimum quality score [25]

-m      Minimum mapping quality score [25]

-O      Minimum homoplymeric length [5]

-s      Infer strand (for strand oriented reads) [1]. It indicates which read is in line with RNA. Available values are: 1:read1 as RNA,read2 not as RNA; 2:read1 not as RNA,read2 as RNA; 12:read1 as RNA,read2 as RNA; 0:read1 not as RNA,read2 not as RNA.

-g      Strand inference type 1:maxValue 2:useConfidence [1]; maxValue: the most prominent strand count will be used; useConfidence: strand is assigned if over a prefixed frequency confidence (-x option)

-x      Strand confidence [0.70]

-S      Strand correction. Once the strand has been inferred, only bases according to this strand will be selected.

-G      Infer strand by GFF annotation (must be sorted, otherwise use -X). Sorting requires grep and sort unix executables.

-X      Sort annotation files. It requires grep and sort unix executables.

-K      File with positions to exclude (chromosome_name coordinate)

-e      Exclude multi hits

-d      Exclude duplicates

-p      Use paired concardant reads only

-u      Consider mapping quality

-T      Trim x bases up and y bases down per read [0-0]

-B      Blat folder for correction

-U      Remove substitutions in homopolymeric regions

-v      Minimum number of reads supporting the variation [3]

-n      Minimum editing frequency [0.1]

-E      Exclude positions with multiple changes

-P      File containing splice sites annotations (SpliceSite file format see above for details)

-r      Num. of bases near splice sites to explore [4]

-h      Print the help

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