Adding Checking Points

[ChristopheLegendre]

Hi Abigail,

Thanks for providing us the Rscript filteringcalls_dbsnp_tester_withsnpeff.R you worked on to filter the calls according to Sam's specifications.

Here are some comments and suggestions:

• Could you add some comments to the most important steps of the process?
• Could you add some checking points and make sure that the input VCF file provided has the expected TAGs and Fields you need to process the records (aka variant line)?
• May you add a line stipulating that the version of R should be 4.0 or up? The current version of VariantAnnotator requires R>=4.0.0
• You may remove loading the following libraries since they are already included in the tidyverse one: tidyr and dplyr.
• You must be careful when using some of the function. I noticed that lots of function are in conflicts with each other because from one package to the other they have the same name. See the information displayed in terminal when loading the packages. If you use function that are common to two packages, you must prefix that function with the package name to make sure that this is the one function you want to use. NOTE: I saw you did it when using select from dplyr :-)

Questions:

• Why is there the genomic version in the line you read the vcf in ? vcf <- readVcf(args[1], "hg19")
• Do we MUST have data in the VCF aligned and called using the reference genome "GRCh37", aka hg19? We use GRCh38. Do we need to update script to run it with GRCh38?

ERROR:

I got this ERROR: Error in h(simpleError(msg, call)) : error in evaluating the argument 'args' in selecting a method for function 'do.call': error in evaluating the argument 'x' in selecting a method for function 'strsplit': object 'GENEINFO' not found Calls: within ... strsplit -> .handleSimpleError -> h -> .handleSimpleError -> h Execution halted

I think this is related to my comment above by letting the user know what fields and tags are mandatory or speciffy if the annotation has to be performed using snpEff or VEP. I guess you used a snpEff-annotated VCF, didn't you?

• Can you tell me where the GENEINFO tag come from? and What are the Values associated with that tag?

Thanks, Best, Christophe

[aahowel3]

Hi Chris,

Sorry for the delay I was out of town last week, absolutely I can make those edits to my script and push them.

No it works the same either way I don't think we need the hg19 argument.

The error is probably because the VCF in use doesn't have a GENEINFO column, I've been using snpEFF annotated files I don't know if VEP has that column, I'll double check.

Best, Abby

On Wed, Aug 24, 2022 at 11:16 AM Chris @.***> wrote:

Hi Abigail,

Thanks for providing us the Rscript filteringcalls_dbsnp_tester_withsnpeff.R you worked on to filter the calls according to Sam's specifications. Here are some comments and suggestions:

• Could you add some comments to the most important steps of the process?
• Could you add some checking points and make sure that the input VCF file provided has the expected TAGs and Fields you need to process the records (aka variant line)?
• May you add a line stipulating that the version of R should be 4.0 or up? The current version of VariantAnnotator requires R>=4.0.0
• You may remove the load of the following libraries since they are already included in the tidyverse one: tidyr and dplyr.
• You must be careful when using some of the function. I noticed that lots of function are in conflicts with each other because from one package to the other they have the same name. See the information displayed in terminal when loading the packages. If you use function that are common to two packages, you must prefix that function with the package name to make sure that this is the one function you want to use.

Questions:

• Why is there the genomic version in the line you read the vcf in ? vcf <- readVcf(args[1], "hg19")
• Do we MUST have data in the VCF aligned and called using the reference genome "GRCh37", aka hg19? We use GRCh38. Do we need to update script to run it with GRCh38?

ERROR:

I got this ERROR:

error in evaluating the argument 'args' in selecting a method for function 'do.call': error in evaluating the argument 'x' in selecting a method for function 'strsplit': object 'GENEINFO' not found Calls: within ... strsplit -> .handleSimpleError -> h -> .handleSimpleError -> h Execution halted```

I think this is related to my comment above by letting the user know what fields and tags are mandatory.

Can you tell me from where the GENEINFO tag come from?

Thanks, Best, Christophe

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-- Abigail Howell

Arizona State University | Barrett Honors College | Class of 2017

Biological Sciences (Biomedical Sciences), BS

Ph.D. Candidate, Molecular and Cellular Biology

Arizona State University

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