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Update of DNAscan.py #6

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  1. Changed formatting of @rg fields so it is compatible with BWA-MEM
  2. Updated intensive mode so compatible with GATK 4.1.9.0 (jar version) with HaplotypeCaller, and changed deprecated CombineVariants to MergeVcfs
  3. Updating clinvar in ALSGeneScanner to clinvar_20200316
  4. Other minor changes include:
    • making it possible to generate several java services at the same time i.e. sequencing report in intensive mode
    • changing annotation to be compatible with hg38
    • debugging minor errors in script

Extra Notes

  • If you want to use the provided variant catalog.json for ExpansionHunter with test data, you need to open the file and delete the first 2-3 lines before the main json content for it to work
  • The default filter_string option is too strict for the test data, therefore need to add -filter "custom options" as highlighted in the DNAscan README

@hevmarriott
Update of DNAscan.py
448eab6 
1. Changed formatting of @rg fields so it is compatible with BWA-MEM 
2. Updated intensive mode so compatible with GATK 4.1.9.0 (jar version) with HaplotypeCaller, and changed deprecated CombineVariants to MergeVcfs 
3. Updating clinvar in ALSGeneScanner to clinvar_20200316 
4. Other minor changes include:
    - making it possible to generate several java services at the same time i.e.  sequencing report in intensive mode
    - changing annotation to be compatible with hg38 
    - debugging minor errors in script

Extra Notes
- If you want to use the provided variant catalog.json for ExpansionHunter with test data, you need to open the file and delete the first 2-3 lines before the main json content for it to work
- The default filter_string option is too strict for the test data, therefore need to add -filter "custom options" as highlighted in the DNAscan README
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