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Created with Raphaël 2.2.019Dec12430Nov2831Oct2431Aug29221817161523Jun2216141312922May121014Apr31Mar291510Feb8Dec12Oct15Sep24Aug16151043231Jul2813121129Jun2221178731May25242320191812104219Apr1312129Mar2325Feb2324Jan1314Dec13723Nov221918171615227Oct1486542130Sep29730Aug2623181321Jul1418Jun153May230Apr29723Mar15Feb8Dec27Oct30Sep28239328Aug27262524191730Jun10Feb69Jan826Nov2518Oct171625Sep23Fixed path for QC report dataFixed path for QC report dataFixed PATH for bcbio toolsbatch id no longer needed for PED checkMerge branch 'u035-prod' of git.ecdf.ed.ac.uk:igmmbioinformatics/trio-whole-exome into u035-prodbinding the prod folder for singularity IGVUpdate SOP_filezilla_setup.mdUpdated production data/analysis locations to u035-prodRemoved Nextflow scripts from u035-prod branchUpdated u035 -> u035-prod for production data and analysisUpdated u035 -> u035-prod for production data and analysisUpdated download scripts for new method from EdGeSet image widthKevin_BranchKevin_BranchTest width for imagesAdd screenshots to filezilla sopImage for filezilla SOPImage for filezilla SOPImage for filezilla SOPAdd new directoryAdded SOP for FileZilla setup draftAdded Mike scripts for redoing setupDocumentation of running script for generating singletons from duos and prioritization order of familiesFixed numbering of stepsRemoved access request statement.Documentation for including reads for samples sequenced on previous runs.Update SOP_sample_transfer_from_CRF_to_EPCC.mdAdded changing permissionsUpload New FileRe-analysis scriptsFirst draft of finding and selecting DECIPHER upload filesAdded fixes for gatk haplotype parameters and results dirRe-running VEP if neededAdded VEP effects to configChanged sort order of families by batch instead of date, added steps for setting parent field to 0 for shared-affected families, description of step for DECIPHER upload file copyFixed position of defining SHORT_PROJECT_ID variableRemoving null_if_stubs, fixing write_bcbio_csv, applying changes from c7dff4e8, making run_stubs.sh delete less stuffFixed commented out sectionRe-analysis preparation SOP, scripts, and assets - tested on 20230816_reanalysisFixing argparse in extract_solo_FAM_PRO_ID.py, adding exit statements to IGV in NF script, cleaning up IGV singularity imageUpdated G2P panel