New Command Line Options?

[iamh2o]

There appear to be more command line options in the s/w than you document in the repo. Could you please elaborate on whaat these extra flags do?
~/wgs_resources/bin/TIDDIT.simg TIDDIT.py --sv

usage: TIDDIT --sv --bam inputfile [-o prefix] --ref ref.fasta
[-h] [--sv] --bam BAM [-o O] [-i I] [-d D] [-p P] [-r R] [-q Q] [-Q Q]
[-n N] [-e E] [-l L] [-s S] [-z Z] [--force_ploidy] [--no_cluster]
[--debug] [--n_mask N_MASK] [--ref REF] [--p_ratio P_RATIO]
[--r_ratio R_RATIO]
TIDDIT --sv --bam inputfile [-o prefix] --ref ref.fasta: error: argument --bam is required

Thank you!

John Major

[J35P312]

Hello!
Sorry for the delay, I noticed there is an issue in printing the help module, I will fix it tomorrow. Here's a list and some information on all of the commands in the SV module. Feel free to ask if you have any questions regarding these options!

--bam BAM coordinate sorted bam file(required)

-o O output prefix(default=output)

-i I paired reads maximum allowed insert size. Pairs aligning on the same chr at a distance higher than this are considered candidates for SV (default= 99.9th percentile of insert size)

-d D expected reads orientations, possible values "innie" (-><-) or "outtie" (<- ->). Default: major orientation within the dataset

-p P Minimum number of supporting pairs in order to call a variation event (default 3)

-r R Minimum number of supporting split reads to call a small variant (default 3)

-q Q Minimum mapping quality to consider an alignment (default 5)

-Q Q Minimum regional mapping quality (default 20)

-n N the ploidy of the organism,(default = 2)

-e E clustering distance parameter, discordant pairs closer than this distance are considered to belong to the same variant(default = sqrt(insert-size*2)*12)

-l L min-pts parameter (default=3),must be set >= 2

-s S Number of reads to sample when computing library statistics(default=25000000)

-z Z minimum variant size (default=100), variants smaller than this will not be printed ( z < 10 is not recomended)

--force_ploidy force the ploidy to be set to -n across the entire genome (i.e skip coverage normalisation of chromosomes)

--no_cluster Run only the TIDDIT signal extraction

--debug rerun the tiddit clustering procedure

--n_mask N_MASK exclude regions from coverage calculation if they contain more than this fraction of N (default = 0.5)

--ref REF reference fasta, used for GC correction and for reading cram

--p_ratio P_RATIO minimum discordant pair/normal pair ratio at the breakpoint junction(default=20)

--r_ratio R_RATIO minimum split read/coverage ratio at the breakpoint junction(default=10)

Best regards
//Jesper

[iamh2o]

Thanks!