Updated analyse_list_of_samples.py #7
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hevmarriott wants to merge 2 commits intoKHP-Informatics:masterfrom
Open
Updated analyse_list_of_samples.py #7hevmarriott wants to merge 2 commits intoKHP-Informatics:masterfrom
hevmarriott wants to merge 2 commits intoKHP-Informatics:masterfrom
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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
1. Paths module replaced with paths_configs 2. Python path removed and replaced with python3 in command line
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As well as updating DNAscan.py, the list_of_samples script should also work for multiple samples.