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?
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?
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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