UMCUGenetics/Dx_resources

Issues

• Family IGV.session

  #51 opened 4 years ago by melferink
  1

• IGV session layout

  #58 opened 4 years ago by melferink
  1

• Sort in make_BEDdetail.py is incorrect

  #78 opened 4 years ago by melferink
  1

• 1-based position in .igv output file

  #70 opened 2 years ago by melferink
  0

• UCSC BED file: include prefix in "track name="

  #80 opened 4 years ago by melferink
  0

• Correction for DEL with ratio >1 can result in double events

  #79 opened 4 years ago by melferink
  0

• Include SampleID in files instead of BAMID

  #54 opened 4 years ago by melferink
  1

• Add used BED tracks (i.e. HC file) to VCF metadata

  #61 opened 4 years ago by melferink
  2

• Add female/male status option to submit_batch_exomedepth.py

  #66 opened 4 years ago by melferink
  1

• Add merge warning to CNV QC if merge sample

  #67 opened 4 years ago by melferink
  1

• Alissa count file

  #73 opened 4 years ago by melferink
  1

• Include inheritance mode

  #37 opened 5 years ago by melferink
  0

• Update README

  #64 opened 4 years ago by melferink
  1

• Make female/male choice in argparse ed_csv_to_vcf.py

  #68 opened 4 years ago by melferink
  1

• make_BEDdetail.py gives incorrect count in header UCSC/IGV bed file

  #75 opened 4 years ago by melferink
  0

• Add OptionParser to R code

  #76 opened 4 years ago by melferink
  0

• Difference in reference genome path re-analysis vs normal

  #72 opened 4 years ago by melferink
  1

• Increase minumum setting gender_determination_y_ratio

  #71 opened 4 years ago by melferink
  0

• nrows my.counts is -1

  #65 opened 4 years ago by melferink
  2

• Exomdepth > Exomedepth typo in VCF tempate

  #52 opened 4 years ago by melferink
  1

• Add license

  #56 opened 4 years ago by melferink
  0

• Add RefSet to BEDdetail HTML

  #60 opened 4 years ago by melferink
  0

• UPD track in IGV

  #43 opened 4 years ago by melferink
  0

• Include analysis name in VCF name

  #48 opened 4 years ago by melferink
  1

• Include larger default expectedCNVlength

  #46 opened 4 years ago by melferink
  0

• Codeblock for virtualenv in ExomeDepth README

  #45 opened 4 years ago by melferink
  0

• Mean (delta ratio) van alle target

  #47 opened 4 years ago by melferink
  1

• update to Argparse.

  #31 opened 4 years ago by melferink
  1

• refset parameter not working in submit_batch_exomedepth.py

  #34 opened 4 years ago by melferink
  0

• ED: include start region in session

  #39 opened 4 years ago by melferink
  0

• Implement argparse

  #30 opened 4 years ago by melferink
  0

• Regions of Homozygosity track

  #42 opened 4 years ago by melferink
  0

• Combine CNV and SNV VCF files

  #41 opened 4 years ago by melferink
  0

• Allele frequency plot (SNV/INDEL VCF) into IGV session

  #38 opened 5 years ago by melferink
  0

• BAF plot based on VAF + track in IGV session

  #33 opened 5 years ago by melferink
  0

• Use GATK (only) in perform_RTGtools.py

  #18 opened 8 years ago by melferink
  0

• Improvements perform_RTGtools.py

  #16 opened 8 years ago by melferink
  0

• Help menu parameter -o in perform_RTGtools.py says indel instead of snp

  #15 opened 8 years ago by melferink
  0

• Remove NEU02 in gpanel list

  #14 opened 8 years ago by melferink
  0

• Add gene panels

  #17 opened 8 years ago by melferink
  0

• Add MET03 Panel

  #13 opened 8 years ago by melferink
  0

• Improve regex WISECONDOR_testing.sh

  #12 opened 8 years ago by melferink
  0

• Increase time slot for CALLING_TIME and CALLING_MASTER_TIME

  #11 opened 8 years ago by melferink
  0

• Discontinue PbT for Exomes (VCFUTILS_PHASE no)

  #10 opened 8 years ago by melferink
  0

• remove gene-panels

  #6 opened 8 years ago by melferink
  0

• Add

  #7 opened 8 years ago by melferink
  0

• Add complete gene panels Nierziekte

  #8 opened 8 years ago by melferink
  0

• Change OBE00 > add gene GNAS

  #9 opened 8 years ago by melferink
  0

• Add replacement in cleanup scripts: "," for "." in exoncov tsv files

  #5 opened 9 years ago by melferink
  0

• Add NEU01 to panels

  #4 opened 9 years ago by melferink
  0