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How do you generate the file required for the --contig-ploidy-priors parameter

I have been attempting to use the new germlineCNV caller tool and compare it the XHMM but am having a very difficult time running the DetermineGermlineContigPloidy function in cohort mode in gatk. My trouble arises from the requirment for --contig-ploidy-priors parameter. It requires a TSV file of prior probabilities for each integer ploidy state and for each contig, but am unsure on how to generate this file for my data. What does this file require? How do you know the prior probabilities? I have tried using the suggested table from previous posts :
CONTIG_NAME PLOIDY_PRIOR_0 PLOIDY_PRIOR_1 PLOIDY_PRIOR_2 PLOIDY_PRIOR_3
1 0.0 0.01 0.98 0.01
2 0.0 0.01 0.98 0.01
3 0.0 0.01 0.98 0.01
4 0.0 0.01 0.98 0.01
5 0.0 0.01 0.98 0.01
6 0.0 0.01 0.98 0.01
7 0.0 0.01 0.98 0.01
8 0.0 0.01 0.98 0.01
9 0.0 0.01 0.98 0.01
10 0.0 0.01 0.98 0.01
11 0.0 0.01 0.98 0.01
12 0.0 0.01 0.98 0.01
13 0.0 0.01 0.98 0.01
14 0.0 0.01 0.98 0.01
15 0.0 0.01 0.98 0.01
16 0.0 0.01 0.98 0.01
17 0.0 0.01 0.98 0.01
18 0.0 0.01 0.98 0.01
19 0.0 0.01 0.98 0.01
20 0.0 0.01 0.98 0.01
21 0.0 0.01 0.98 0.01
22 0.0 0.01 0.98 0.01
X 0.01 0.49 0.49 0.01
Y 0.495 0.495 0.01 0.0

But this produces an error of "AssertionError: Some contigs do not have ploidy priors"

I do not understand why. Can someone shed some light on this?

Best Answer

Answers

  • mtkk94mtkk94 Member
    edited May 2019

    How do I generate this table? What does the values mean?

    Post edited by mtkk94 on
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