Variant Analysis

Usage -i rnaseq.bam -f reference.fa



-i      BAM file

-I      Sort input BAM file

-f      Reference in fasta file

-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.

-b      Use input distribution file

-a      Fisher Tail [l, r, t] [default l] [l=left_tail, r=right_tail, t=two_tail]

-c      Min. read coverage [10]

-Q      Fastq offset value [33]

-q      Min. quality score [25]

-m      Min. mapping quality score [25]

-O      Min. 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)

-X      Sort annotation files

-K      File with positions to exclude

-e      Exclude multi hits

-d      Exclude duplicates

-l      Select significant sites

-V      Significant value [0.05]

-w      Statistical test [BH, BO, NO] [default BH] [BH=Benjamini, BO=Bonferroni, NO=No Correction]

-U      Use specific substitutions separated by comma [example: AG,TC]

-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

-W      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      Number of bases near splice sites to explore [4]

-h      Print the help

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