Question: How to generate the contigs ploidy priors table (yeast) for GATK DetermineGermlineContigPloidy --contig-ploidy-priors option ?
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gravatar for mikizu
4 months ago by
mikizu0
France
mikizu0 wrote:

Hi !

I was asked to determine the ploidy level and to do CNV calling on a yeast sample (Reference sequence : S. cerevisiae S288C).

In order to perform CNV calling with the GATK pipeline "(How to) Call common and rare germline copy number variants", in the third step the tool "DetermineGermlineContigPloidy [BETA]" has to be used and a "contig ploidy priors" table file is requested for the option --contig-ploidy-priors. However, after having searched for some answers to my question (the answer may be obvious ? This is the first time I am doing this), I still do not know how to create or generate this file.

Here is the kind of table that I should use :

CONTIG_NAME PLOIDY_PRIOR_0 PLOIDY_PRIOR_1 PLOIDY_PRIOR_2 PLOIDY_PRIOR_3

1 0.01 0.01 0.97 0.01

2 0.01 0.01 0.97 0.01

X 0.01 0.49 0.49 0.01

Y 0.50 0.50 0.00 0.00


Here are some GATK topics about the --contig-ploidy-priors I have already consulted :


Does anyone know or have an idea about how to generate/create this contig ploidy priors table ? Do I have to create a random table and put the numbers I think are good thanks to a ploidy detection that I should perform before ? Do you think that I should just use CNVnator, CNVkit or any other tool for only "tumor"/one sample CNV calling ?

Thank you in advance, any help would be appreciated.

gcnv cnv gatk variant-calling • 363 views
ADD COMMENTlink modified 20 days ago by xoaib0 • written 4 months ago by mikizu0

Did you get any solution? How to make this table?

ADD REPLYlink written 20 days ago by xoaib0
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