Skip to content
Snippets Groups Projects
Select Git revision
  • Kevin_Branch
  • emma-cnv
  • master default protected
  • mwham_develop
  • u035-prod
  • ultra_last_commit
  • old_ultra_archive
7 results
You can move around the graph by using the arrow keys.
Created with Raphaël 2.2.023Jun2216141312922May121014Apr31Mar291510Feb8Dec12Oct15Sep24Aug16151043231Jul2813121129Jun2221178731May25242320191812104219Apr1312129Mar2325Feb2324Jan1314Dec13723Nov221918171615227Oct1486542130Sep29730Aug2623181321Jul1418Jun153May230Apr29723Mar15Feb8Dec27Oct30Sep28239328Aug27262524191730Jun10Feb69Jan826Nov2518Oct171625Sep23Fixing split_trio_solo_variants.pyAdding png splitting stage and NHS output dirFixing IGV/xvfb/Singularity. Using absolute paths in snapshot files. Adding bam indexes to channelsDisentangling spaghetti. Removing old prioritisation process, merging prioritisation and setup, using watchPath/fromPath to pick up or wait for decipher file. Adding igv stub. Adding fake test asset filesMerge branch 'variant_prioritisation' into 'master'Merge branch 'master' into 'variant_prioritisation'Added GATK Haplotype new parameters on active probability threshold and interval paddingFixing stub testsFixing dnu_cleanAdding strand bias correction from process_trio.shMerge branch 'master' of git.ecdf.ed.ac.uk:igmmbioinformatics/trio-whole-exome into variant_prioritisationAdding programs.txt, fixing some prioritisation output locationsFS/SOR filtering/flagging for fetal anomaliesFixing g2p and decipher file generationFixing decipher scripts for Nextflow, adding genome reference dict and VEP params, fixing Conda. Splitting denovo VCF filtering from VASESegmenting variant prioritisation, adding stub tests. Making Conda optional when running stubs. Making prioritisation scripts executable, compatible with Nextflow channels.Merge branch 'master' of git.ecdf.ed.ac.uk:igmmbioinformatics/trio-whole-exomeUpdated prioritization scripts to include FS/SOR flag filteringScripts for computing DDD coverage statsFixing prioritisation outputs, adding bam index, making prioritisation console output less spammyVar prioritisation/cram compression fixes. Fixing BCBio output collation. Adding var prioritisation GiaB testFixed peddy validation script paramsUpdated processing scriptsMerge branch 'master' of git.ecdf.ed.ac.uk:igmmbioinformatics/trio-whole-exomeAdded CCDS to BED conversion scriptUpdated CCDS versionMerge branch 'master' of git.ecdf.ed.ac.uk:igmmbioinformatics/trio-whole-exome into variant_prioritisationAdding fake DECIPHER data, applying changes to process_trio.sh for NextFlowPulling in process_*.sh changes from Ultra 2, adapting process_trio.sh for NextFlow. Making medium jobs 8cpu/16Gb, adding small_medium for 4cpu/8Gb. Fixing bcbio family stub. Adding stubs and channel processing for variant prioritisation inputs. Simplifying stub tests.Merge branch 'master' of git.ecdf.ed.ac.uk:igmmbioinformatics/trio-whole-exomeAdded reanalysis scripts from MikeUpdated path of bcbio template to assets folderAdded error check in case no ped_check.csv files found for a familyFixing scripts pathCleaned up old prioritization scriptsCleaned up old prioritization scriptsRefactored to use tuples for passing linked information through channels, parameterized some hard-coded valuesemma-cnvemma-cnvAlternative samplesheet for cnv calling - bam/bai files instead of fastq1/fastq2Tidied up some unneeded print statements and commentsRemoved package installation, chromosome prefix removal, fixed output directory trailing slash