Three questions about calling CNV in Germline.
AnsweredQuestion 1:
I noticed that there is a sentence in the description of GermlineCNVCaller:
providing a cohort of germline samples sequenced using the same sequencing platform and library preparation protocol (in case of WES, the same capture kit).
I downloaded SRA data from two different articles, that is, I have two batches of data. What should I do?
Should I separate the two batches of data instead of mix of them together in process of DetermineGermlineContigPloidy and GermlineCNVCaller?
That is, should I do twice operations in the DetermineGermlineContigPloidy and GermlineCNVCaller process respectively?
Question 2:
What if the ploidy result of DetermineGermlineContigPloidy is known to be wrong by other means?
For example, the ploidy of a chromosome of certain sample is known to be 2 by means of flow cytometry or other ways, but the result given by DetermineGermlineContigPloidy is 3. Can I change the contig_ploidy.tsv result file from 3 to 2?
Question 3:
Does PostprocessGermlineCNVCalls generate VCF file only containing one sample information at a time?
How can I get a VCF file containing multiple sample information?
Thanks for reply.
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Yes, the JointGermlineCNVSegmentation tool was released in 4.2.0.0. There are release notes available here: https://github.com/broadinstitute/gatk/releases/tag/4.2.0.0
Here are some notes as it was being built as well: https://github.com/broadinstitute/gatk/pull/6554
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Hi rq m,
Here are the answers to your three questions, hope this helps!
- Yes, you should run these batches separately.
- Yes, you can change the ploidy in that file.
- Run GATK 4.2.
Best,
Genevieve
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Hi Genevieve Brandt.
Thanks for your answer.
I have understood question 1 and 2, but I still have doubts about question 3.
I have used version 4.2. I called CNV according the tutorial (How to) Call common and rare germline copy number variants.In the end, I generated many VCF files. But, each VCF file contains only one sample CNV information. How can I get all samples CNV information in ONE VCF file, like calling SNP?
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There is a new tool called JointGermlineCNVSegmentation. There is no clear documentation available yet but you can try. I will be trying it in a few days.
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Hi, I have one confusion, how to change the ploidy of a chromosome to 2 from 3.
Is the example below is right?
CONTIG_NAME PLOIDY_PRIOR_0 PLOIDY_PRIOR_1 PLOIDY_PRIOR_2 PLOIDY_PRIOR_3 I 0.01 0.98 0.01 0 II 0.01 0.98 0.01 0 III 0.01 0.98 0.01 0 -
Hi Archana Verma,
Yes, this should work. Setting the prior probability to 0 will remove that ploidy state and forbid the tool from assuming a ploidy of 3. There is additional information in the DetermineFermlineContigPloidy Tool Documentation. Please let me know if this answers your question.
Kind regards,
Pamela
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Hi Pamela Bretscher,
Thanks for your answer.
I have understood the explanation.
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