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J35P312 / TIDDIT

TIDDIT - structural variant calling
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Ploidy #6

Open Thatguy027 opened 6 years ago

Thatguy027 commented 6 years ago

Hi there,

This is more of an inquiry than an issue.

I just cam across your paper describing TIDDIT and wanted to give your software a test. I am wondering how to deal with ploidy. Though the organism I work with is a diploid (C. elegans), it is a (mainly) hermaphroditic species and therefore homozygous throughout its genome. When using other variant callers I usually set the ploidy to 1 when the option is available.

I downloaded and installed TIDDIT and am not seeing a ploidy flag in the additional options. Am I missing something? Or do you recommend applying post-calling depth/support filters to the variant set.

Thank you for your time, Stefan

Thatguy027 commented 6 years ago

Ah.. Seems like -n is the parameter I am looking for!

J35P312 commented 6 years ago

Hello! That's correct, the -n parameter will allow you to set the ploidy! You should also set the chromosomes listed by the -s parameter to a few chromosomes that are in your genome. For example:

python TIDDIT.py --sv --bam input.bam -n 1 -s 1,2,3

or similar, make sure to check that the chromosomes 1,2,3 really are in your bam file, otherwise you will get a reference mismatch error! Good luck, and feel free to ask if you run in to any problems, I know the documentation needs a bit of fixing!

//Jesper

splaisan commented 5 years ago

Hi @J35P312 are you sure it is -s? v2.7.1

Usage: TIDDIT --sv -b inputfile [-o prefix] Other options -b coordinate sorted bam file(required) -i paired reads maximum allowed insert size. Pairs aligning on the same chr at a distance higher than this are considered candidates for SV (=3std + mean_insert_size) -d expected reads orientations, possible values "innie" (-> <-) or "outtie" (<- ->). Default: major orientation within the dataset -p Minimum number of supporting pairs in order to call a variation event (default 3) -r Minimum number of supporting split reads to call a small variant (default 3) -q Minimum mapping quality to consider an alignment (default 10) -c average coverage, (default= computed from the bam file) -s Number of reads to sample when computing library statistics, (default= 100000000) -n the number of sets of chromosomes,(default = 2) -m minimum variant size,(default = 100)

J35P312 commented 5 years ago

Hello there! Use the -n option to change the ploidy:

TIDDIT.py --sv --bam test.bam -n 3

if you are analysing a triploid organism for instance. Good luck!