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Confusing documentary in regard to SNP input files #11
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I will later update the readme to better describe the differences. But now I will give you a brief description: First of all, there are two layers of cmdline, one is for the wrapper FASTQuick.sh the other is for the underlying binary executable programs. It’s recommended to stick with FASTQuick.sh arguments which is simplified based on binary executables' arguments. Now back to your question
Hope this answer your question. |
Hi,
I am interested in the tool, but find parts of the documentation somewhat confusing.
Could you maybe clarify the difference between these options:
--siteVCF
--candidateVCF
--predefinedVCF
--dbSNP
--dbsnpVCF
--SVDPrefix
--RefVCF
--RefVCFList
And the difference between:
--callableRegion
and
--regionList
siteVCF (for candidate sites in the wiki) and predefinedVCF (for predefined sites) are used in the index function, so I assume they contain the SNPs to build the reduced region as written in the paper, which is also filtered by either callableRegion and regionList, but what exactly is the difference between candidates and predefined sites and what is the difference between target region and callable region?
In the main Readme file you use dbSNP, in the wiki you have dbsnpVCF as option. Is that a type or are there two options. If there is only one option, how is this VCF file handled differently from the candidate or predefined sites?
Also in the examples the candidateVCF option is used, which is not found in the wiki.
The same goes for RefVCFList.
I would appreciate if you could take the time explain what the each option does.
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