scholl-lab / vcf-filtering Goto Github PK

When we convert the tsv values using replace_gt_with_sample.sh and the GT field has only numbers and they are separated by comma, excel converts these to numbers.

Solution:

• add an argument to set the separator
• change default to ";"

This should inlcude SnpSift, awk, sed, tee and bash.
In the R script add echo messages for the package version and R vesrion runnig.

Similar to the output from "sed --version".
Plus add sccript author information.

To make usage easier, the repository README should include instructions on how to install required tools and libraries, such as conda.

Use our final script "filter_phenotypes.sh" in "filter_variants.sh" to output the phenotypes of all filtered samples. If the xlsx flag is set, the output of filter_phenotypes.sh should be in a separate sheet. If the output is TSV (the default), it will be two files with the same basename and ".phenoytpes" appended before the "filter_phenotypes.sh" output. If the output is stdout, the phenotypes should not be printed. In general, there should be an optional flag to request phenotypes. Also, the location of the "filter_phenotypes.sh script and the input-file argument to it should be added as arguments to this script.

TODO:

• Add new arguments: Add arguments to specify the location of the "filter_phenotypes.sh" script, the phenotype input file, and a flag to request phenotype output.
• Handle new arguments and conditions: Modify the "filter_variants.sh" script to parse and handle these new arguments. Include logic to call "filter_phenotypes.sh" under the appropriate conditions.
• Manage output formats: Handle different output scenarios (XLSX, TSV, STDOUT) as specified.
• Requires #10

Add an option to filter by position or for specific variants instead of gene name; check the reference allele for input variants.

The script can produce unexpected output If the GT field does not contain VCF style genotypes.
Implement a check for correct data format in this column.

The -V and -h options do not appear to be implemented in args or long to short argument handling.

Make tsv_to_excel.R location an argument with defaults.

For conversion, the script "tsv_to_excel.R" should accept various separated file formats (including csv).

TODO:

• add argument to explicitly set the separator
• Include logic to determine the separator based on the file extension.
• Include validation logic
• rename script accoringly (maybe convert_to_excel.R)

Make the script handle CSV or TSV files with different delimiters. Add an option to specify the delimiter (output). This makes the script more flexible in dealing with various file formats.

Add a script that will generate screenshots of the variants' alignment in the IGV browser so that it can be validated. This should be done for all the variants passing filtering. The screenshot should include at least one control.

TODO:

• check for existing implementations and tools
• check if IGV is suitable for this task
• check what scriping language to use
• decide for a format of the screenshots
• decide for a file naming convention
• decide for a folder structure
• Implement the script

Add semantic versioning and a version flag to replace_gt_with_sample.sh

Add help message as default when passing no arguments to have the same behaviour as the other scripts.

Currently all arguments for "replace_gt_with_sample.sh" are hardcoded. To allow more flexibility there should be ar argument to pass script specific setting from the master script.

For reproducibility it would be helpful to add meta information to the Excel output including filter setting and column documentation.

TODO:

• for filter_variants.sh
• for filter_variants.sh
• for replace_gt_with_sample.sh
• for tsv_to_excel.R

Include in all scripts the requirements and software or package versions that have been tested.

The scripts should also echo their name and this should be set as a variable in each script.

• Include an argument to set the sheet name in the excel file. This should have a default value.
• Instead of overwriting, add an argument to add the sheet to an existing excel file.
• Add logic to not overwrite existing sheets with the same name if they already exist, but instead add a number as an iterator.

Needed for #4

Currently the default values overwrite the config values in the script. This is not the expected or intended behaviour.

Add basic statistics for the filtered table in echo command.
This could include for example:

• number of variants
• number of samples
• number of genes
• het / hom counts
• type of variants (SNV, indel, missense, lof, etc)