Bioinformatics Core Analysis Tools
  1. Bioinformatics Core Analysis Tools

Utilities

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  1. Bioinformatics Core Analysis Tools
  2. Utilities

Commits

AuthorCommitMessageCommit dateIssues
Richard LupatRichard Lupat
5cfbe1e7792[SEQL-344] Modify Tumour-Normal.vcf sample header for PathOS1.4SEQL-344
Richard LupatRichard Lupat
f192a27b704[SEQL-336] Gene Coverage bug - replace csv.reader with for loopSEQL-336
Richard LupatRichard Lupat
3f1ff961f7f[SEQL-295] Coverage script changes to add min,max,mean,150xSEQL-295
Richard LupatRichard Lupat
c4b1716af5bSEQL-276 averageAD_DP.pySEQL-276
Richard LupatRichard Lupat
e279fe0ab61SEQL-228 Seqliner v0.4 release bug fixesSEQL-228
Jason LiJason Li
889367c7e6afixed mouse human hugo symbol mapping alias problem -- now pick map with best support
Jason LiJason Li
cf50fbaa72dadded tool to remove ambiguity codes (IUPAC) from vcf
Jason LiJason Li
db58c0a5db8Added mouse-human gene sym mapping based on HUGO HCOP database
RootRoot
71f01ac96e1added pysam
kamarasinghekamarasinghe
dbfcf9c352dAdded galaxy implementation of edgeR
kamarasinghekamarasinghe
bd4b468223cAdded new RNASeQC file to handle Hisat2 output
Richard LupatRichard Lupat
f1c6c6439e0MMerge branch 'master' of ssh://115.146.86.118:7999/bcat/utilities
Richard LupatRichard Lupat
5b7694b1b62Added WGCNV to pmac-utilities-script
Richard LupatRichard Lupat
8812b1ab6adModify geneCoveragePerSample.py to get it to work on new server
Richard LupatRichard Lupat
91eedc0f7f1Add adtex script to Bioinformatics Utilities
Richard LupatRichard Lupat
756ad8616bbMMerge branch 'master' of ssh://115.146.86.118:7999/bcat/utilities
Richard LupatRichard Lupat
ddfe013b338Modify super wrapper scripts
Jason LiJason Li
c563e61cf3badding Ken's vs2vcf.pl to here for docker deployment
Jason LiJason Li
40c4aeca599updated filterTSV and annotateByGeneName
Jason LiJason Li
b6a350ef247updated SUPER automate scripts -- for copying CNV over to PathOS -- tested OK
Richard LupatRichard Lupat
968bb579344Added EXAC scripts
Richard LupatRichard Lupat
f4f20b0c05eAdd EXAC scripts
Jason LiJason Li
101fb461d47updated SUPER wrapper to handle runId suffixes (non pathology samples) and somaticFilter for somatic_v2 pipeline
Jason LiJason Li
eca93a7dea7added script to filter for somatic variants from combined VCF file (with two sample columns -- tumour & germline
Jason LiJason Li
ecf94399b19MMerge branch 'master' of ssh://115.146.86.118:7999/bcat/utilities
Richard LupatRichard Lupat
1cf521222b6Modify annotateBedFile to use ensembl api-ver-73
Jason LiJason Li
805067838aaseqQCpipe changes
Jason LiJason Li
8b2006716c4updated mutation signature scripts
Jason LiJason Li
4b3ee302fa5fixed multi-sample tsv for mutation_signature
Jason LiJason Li
ae4f477b53cadded scripts to analyse transversion/transition / mutation signatures
Jason LiJason Li
b7e743e2509rna_qc_wrapper and fixed seqliner_super_wrapper
Jason LiJason Li
a5865e1ec88added splitVcfBySample
Jason LiJason Li
dbea7a1ba52minor updates to platypus and familial
Jason LiJason Li
c8e15381037MMerge branch 'master' of ssh://115.146.86.118:7999/bcat/utilities
Jason LiJason Li
0aa4d53ddedplatypus wrapper scripts
Jason LiJason Li
cc0124aa37bSUPER automation on cluster completed
Jason LiJason Li
a018eccbd14added copying tumour vcf to tumour -T directory (in addition to -TN)
Jason LiJason Li
855e928de92super wrapper -- modified multiple points to handle germline samples -- includ cnv against hapmap
Jason LiJason Li
639c297f475MMerge branch 'master' of ssh://115.146.86.118:7999/bcat/utilities
Jason LiJason Li
dd1647fc3c2richard lupat original modifications
Jason LiJason Li
92f0944666aadded script to make ADTEx genomewide plot
Jason LiJason Li
bf6f968b1b9added script to use Ensembl API 73 PERL5LIB paths
Jason LiJason Li
60a711141cefixed newline bug
Jason LiJason Li
c33597ac757added add GC content to bed file script; minor updates to annotateByGeneName.pl
Jason LiJason Li
542f032851aadded annotate by Gene Name (add annotation columns given symbols)
Jason LiJason Li
6884c789f18blat query sequence against given bam file
Jason LiJason Li
60a9a2b12e6split bed rows by semi-colons in gene column -- for MuSic ROI
Jason LiJason Li
b70079e58d3new script to add gene symbol to GATK DepthOfCoverage output given bed file
Jason LiJason Li
cb757cc4006Given Ensembl ID, append tsv file with gene symbol and gene name
Jason LiJason Li
463be5e9779script to map between mouse and human symbols (two ways)