Dear GATK team,
Hi I'm Oh.
There seems to be a problem with the tutorial.
I think the samples used in the cohort mode should include a sample used in the case.
However, the tutorial use 24 samples for cohort mode, and suddenly use "cohort-23wgs-20190213-contig-ploidy-model" when executing case mode.
Additionally, I have a question.
I have a sample of 200 disease group and 100 normal group. That is, I have a cohort of 300 samples.
What I ultimately want to do is compare the germline CNV of the disease group and the normal group.
In this case, please tell us which analysis method is more suitable.
Is it better to create a gCNV model in COHORT mode using 300 samples, and perform it individually for 200 disease groups and 100 normal groups using CASE MODE?
(1) COHORT mode using 300 samples, and
(2) CASE mode by one sample (n=300)
(3) Compare CNV between 200 disease group and 100 healthy group
Or, it is correct to perform COHORT gCNV using 300 samples and see the results.
(1) COHORT mode using 300 samples, and compare CNV between 200 disease group and 100 healthy group.
Many Thanks, Oh.
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