ntm
commented
2 years ago I'm not sure if the coverage info is really useful, that's why I didn't package or document it cleanly (eg --help).
Basically it uses the classical/simple way of getting its arguments rather than the more powerful arg parsing with GetOpt, ie instead of e.g. --arg1 val1 --arg2 val2 , you just call the script with the arguments in the order expected by the script.
Example:
perl 0_coverage.pl sampleCLN.xlsx yourCandidateGenes.xlsx canonicalTranscripts_220717.tsv.gz grexome0001.g.vcf.gz CoverageDir/
You would have to prepend the appropriate path for each file.
You would also need to run this command once for each GVCF.
And since this script uses the Bio::DB::HTS::Tabix module, you need to have a working copy of this module, accessible to the script. In my case this module is built when installing/updating VEP, and is available in the VEP install subdir. On my systems this is: /home/nthierry/Software/VariantEffectPredictor/ensembl-vep/. However since this subdir is not in my default PERL search path, I hardcoded it with use lib "path/to/ensembl-vep/";. You may need to do the same.
But really, this coverage info is not super useful in my opinion.
Chris-lang478
@ntm I am trying to follow your instruction in 0_coverage.pl to make coverage files. I am so new to perl language. And perl 0_coverage.pl --help is empty. I don't know how to add the samples xlsx, candidatesFiles $transciptsFile , $gvcf (must be tabix-indexed), and an $outDir.
In your script, it wrote that @ARGV == 5) || die "E $0: needs 5 args: a samples file, a comma-separated list of candidatesFiles, a tsv.gz, a GVCF and an outDir\n"; my ($samplesFile, $candidatesFiles, $transcriptsFile, $gvcf, $outDir) = @ARGV.
What should I do?And there is something like lib "/home/nthierry/Software/VariantEffectPredictor/ensembl-vep/"， Should I modify it? Thanks again!!
Best regards, Chris