imgag/megSAP

Issues

• LongReads: remove unmapped bams

  #247 opened 6 months ago by leonschuetz
  1

• HPO to genes: check if HGMD helps at all (it has a lot of singletons)

  #265 opened 3 months ago by marc-sturm
  0

• NSX: copy logs of Dragen analysis

  #267 opened 2 months ago by leonschuetz
  0

• bwa-mem2 on newer AMD Servers (srv010)

  #260 opened 3 months ago by leonschuetz
  1

• Getting problem when I type "./download_dbs.sh"

  #266 opened 2 months ago by ThomasYang0615
  0

• Implement trio/multi

  #221 opened 10 months ago by marc-sturm
  9

• Improve PRS computation

  #261 opened 3 months ago by leonschuetz
  1

• No HRD score import on restarted analysis

  #257 opened 3 months ago by leonschuetz
  0

• Test targeted callers with DRAGEN

  #227 opened 9 months ago by marc-sturm
  0

• LongReads: create missing files for older LR samples

  #264 opened 3 months ago by leonschuetz
  0

• LongReads: Create low-confident region

  #263 opened 3 months ago by leonschuetz
  0

• LongReads: Add tool to annotate SR variants to LR GSvar file

  #262 opened 3 months ago by leonschuetz
  0

• Test new Clair3 models

  #243 opened 3 months ago by leonschuetz
  0

• Replace RNA expression analysis by DROP pipeline

  #235 opened 8 months ago by marc-sturm
  0

• make rolled-out megSAP git shared

  #258 opened 3 months ago by leonschuetz
  1

• GSVar improvements for Longread analysis

  #238 opened 6 months ago by caspargross
  1

• No QC when using CRAM

  #256 opened 4 months ago by BeneKenobi
  1

• NovaSeqX: mapping of cfDNA and RNA

  #254 opened 4 months ago by leonschuetz
  0

• Longread vc_clair python environments problems

  #251 opened 5 months ago by alex-seitz
  4

• Check EGFR variant not getting called

  #249 opened 5 months ago by Ott-Alexander
  1

• Variants with pathogenic WT allele

  #239 opened 5 months ago by marc-sturm
  1

• Update megSAP tools and databases

  #233 opened 5 months ago by marc-sturm
  0

• Update Somatic DB/Tools

  #236 opened 5 months ago by Ott-Alexander
  0

• IGV: use JSON genome definition

  #231 opened 5 months ago by marc-sturm
  5

• Annotate gene info from ClinVar

  #237 opened 5 months ago by alex-seitz
  1

• allow custom columns in GSvar

  #248 opened 5 months ago by marc-sturm
  0

• Added SpliceAI details to GSvar

  #246 opened 6 months ago by marc-sturm
  2

• download_dbs.sh throws exception: Reference sequence of variant ... does not match reference bases in genome ...

  #244 opened 6 months ago by leonid-iashin2
  5

• basecalling and alignment on device

  #245 opened 6 months ago by leonschuetz
  1

• Re-calculation of *.cov files after re-mapping

  #241 opened 6 months ago by alex-seitz
  3

• multi-sample calling using gVCF for short-read

  #240 opened 6 months ago by marc-sturm
  0

• Add ROH detection to 'vc'

  #220 opened 6 months ago by marc-sturm
  1

• RNA annotation Indels

  #215 opened a year ago by Ott-Alexander
  0

• Invalid INFO header in annotated Longread VCF

  #234 opened 8 months ago by caspargross
  1

• Run `data_setup.php` at start of each pipeline

  #229 opened 8 months ago by leonschuetz
  0

• megSAP: check if bioinf user is still required for Dragen analysis

  #223 opened 8 months ago by leonschuetz
  0

• Error variant import in `analyze_longreads.php`

  #232 opened 8 months ago by caspargross
  1

• Uncaught ArgumentCountError: ToolBase.php on line 118

  #230 opened 8 months ago by vkulaganathan
  2

• Update precalcualted SpliceAI scores

  #222 opened 9 months ago by marc-sturm
  4

• Add AlphaMissense

  #226 opened 9 months ago by marc-sturm
  0

• Performance validation of difficult genes

  #213 opened 9 months ago by marc-sturm
  0

• Update contamination scores

  #218 opened 9 months ago by marc-sturm
  0

• Test validation datasets

  #224 opened 9 months ago by marc-sturm
  1

• Implement MaxEntScan in own tool

  #217 opened 10 months ago by marc-sturm
  2

• Test high-sensitivity mode on Dragen

  #216 opened a year ago by marc-sturm
  1

• Update of Dragen to version 4.2

  #214 opened a year ago by marc-sturm
  1

• update performance statistics for GRCh38

  #209 opened a year ago by marc-sturm
  0

• add non-patient-specific targeted cfDNA

  #212 opened a year ago by leonschuetz
  0

• Benchmark FANSe

  #211 opened a year ago by Ott-Alexander
  0

• RNA: imprinting & ASE

  #210 opened a year ago by leonschuetz
  0