Commits · 70a4cc11639a7182342bf7a8cc4957386de8e3dd · NGS CLIA Lab / process_scripts

Apr 13, 2020
- Merge branch 'master' of git.biohpc.swmed.edu:ngsclialab/process_scripts · 70a4cc11
  Brandi Cantarel authored 5 years ago
  
  70a4cc11
- fix missing -n option · 33ffd520
  Brandi Cantarel authored 5 years ago
  
  33ffd520
Apr 09, 2020
- update from clinseq · 12ef6163
  Brandi Cantarel authored 5 years ago
  
  12ef6163
- gene abund exon · b78ced98
  Brandi Cantarel authored 5 years ago
  
  b78ced98
- fix license · 2e68c794
  Brandi Cantarel authored 5 years ago
  
  2e68c794
- LICENSE · 0675b9b9
  Brandi Cantarel authored 5 years ago
  
  0675b9b9
- Initial commit · c130bb68
  Brandi Cantarel authored 5 years ago
  
  c130bb68
Apr 07, 2020
- add msisensor2 · 2fa359f8
  Brandi Cantarel authored 5 years ago
  
  2fa359f8
Mar 30, 2020
- update filter cnvkit · 3d9705fc
  Brandi Cantarel authored 5 years ago
  
  3d9705fc
- update viral alignment and mutect filter bug · 50154ca3
  Brandi Cantarel authored 5 years ago
  
  50154ca3
Mar 24, 2020
- updates to load into Answer; CNVKit with Samtools and using haar for small panels · f431810c
  Brandi Cantarel authored 5 years ago
  
  f431810c
Mar 20, 2020
- missing tid for tumoronly workflow · 956a3813
  Brandi Cantarel authored 5 years ago
  
  956a3813
Mar 19, 2020
- update delly svaba sv calling filter · 2f76edc9
  Brandi Cantarel authored 5 years ago
  
  2f76edc9
- filter svaba to have 10kb + in fusion · 7da44e40
  Brandi Cantarel authored 5 years ago
  
  7da44e40
- adding sv- from svaba into dels · 18c85217
  Brandi Cantarel authored 5 years ago
  
  18c85217
- sv filtering · 488f3a25
  Brandi Cantarel authored 5 years ago
  
  488f3a25
Mar 18, 2020
- Merge branch 'master' of git.biohpc.swmed.edu:BICF/Astrocyte/process_scripts · 8d9c724f
  Brandi Cantarel authored 5 years ago
  
  8d9c724f
- pindel filtering path relative to process scripts · 2d64c494
  Brandi Cantarel authored 5 years ago
  
  2d64c494
- update filtering of delly/svaba to separate fusions and indels · 66010ebb
  Brandi Cantarel authored 5 years ago
  
  66010ebb
Mar 12, 2020
- svcalling svaba filtering error AD->AO · c313fc8c
  Brandi Cantarel authored 5 years ago
  
  c313fc8c
Mar 09, 2020
- update svcalling for merging sv and create bed · 85a6fefa
  Brandi Cantarel authored 5 years ago
  
  85a6fefa
Mar 07, 2020
- update file format svcalling · 994ee16a
  Brandi Cantarel authored 5 years ago
  
  994ee16a
- update svcalling for filtering for gene fusion · e56380df
  Brandi Cantarel authored 5 years ago
  
  e56380df
Mar 03, 2020
- updates to sv calling and file naming · 55cfa107
  Brandi Cantarel authored 5 years ago
  
  55cfa107
Feb 19, 2020
- option for manta failure, itdseek in svcalling with filtering · 9eb41f12
  Brandi Cantarel authored 5 years ago
  
  9eb41f12
Feb 18, 2020
- updates for tmp directory, indels, svs and remove hard links to files · e6be1c74
  Brandi Cantarel authored 5 years ago
  
  e6be1c74
Feb 17, 2020

tmp directories for picard commands · e5a78c7e
Brandi Cantarel authored 5 years ago

e5a78c7e

gatk error... · d1591974

Brandi Cantarel authored 5 years ago

gatk error https://gatkforums.broadinstitute.org/gatk/discussion/24492/mutect2-java-lang-illegalargumentexception-cannot-construct-fragment-from-more-than-two-reads#latest

d1591974

Feb 14, 2020
- itdseek with hardcoding · fb9e02ce
  Brandi Cantarel authored 5 years ago
  
  fb9e02ce
- removed hard coded paths to seqprg; update GATK to 4.1.4 · ffd65068
  Brandi Cantarel authored 5 years ago
  
  ffd65068
Feb 12, 2020
- Merge branch 'master' of git.biohpc.swmed.edu:BICF/Astrocyte/process_scripts · 274f44a3
  Brandi Cantarel authored 5 years ago
  
  274f44a3
- add baseDir to trimGalore · 6d29a48f
  Brandi Cantarel authored 5 years ago
  
  6d29a48f
- Merge branch 'master' of git.biohpc.swmed.edu:BICF/Astrocyte/process_scripts · 72c9c152
  Brandi Cantarel authored 5 years ago
  
  72c9c152
- adding option for GRCh37 dnaseqalign and options for SV calling · 8bfcd5b9
  Brandi Cantarel authored 5 years ago
  
  8bfcd5b9
Feb 09, 2020
- missing snpeffgeno option · 6c0e8739
  Brandi Cantarel authored 5 years ago
  
  6c0e8739
Feb 07, 2020
- alter SLURM_CPU_ON_NOCDE = nproc · 244250a0
  Brandi Cantarel authored 5 years ago
  
  244250a0
- filter option trimgalore · 8c413eab
  Brandi Cantarel authored 5 years ago
  
  8c413eab
- add options for alt pon and filtering of itdseek · 9b7a55bd
  Brandi Cantarel authored 5 years ago
  
  9b7a55bd
Feb 05, 2020
- removing fullpaths to biohpc -- made all reference files/directories as options · d40e7697
  Brandi Cantarel authored 5 years ago
  
  d40e7697
Jan 29, 2020
- Merge branch 'master' of git.biohpc.swmed.edu:BICF/Astrocyte/process_scripts · a53c3e20
  Brandi Cantarel authored 5 years ago
  
  a53c3e20