removing fullpaths to biohpc -- made all reference files/directories as options (d40e7697) · Commits · NGS CLIA Lab / process_scripts · GitLab

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NGS CLIA Lab
process_scripts
Commits
d40e7697

Commit d40e7697 authored 5 years ago by

Brandi Cantarel

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removing fullpaths to biohpc -- made all reference files/directories as options

parent a53c3e20

No related merge requests found

Changes 20

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alignment/bamqc.sh 1 addition, 1 deletion

alignment/bamqc.sh
alignment/dnaseqalign.sh 2 additions, 2 deletions

alignment/dnaseqalign.sh
alignment/filter_genefusions.pl 3 additions, 21 deletions

alignment/filter_genefusions.pl
alignment/markdups.sh 13 additions, 5 deletions

alignment/markdups.sh
alignment/rnaseqalign.sh 2 additions, 2 deletions

alignment/rnaseqalign.sh
alignment/starfusion.sh 7 additions, 7 deletions

alignment/starfusion.sh
obsolete/annot_sv.pl 0 additions, 0 deletions

obsolete/annot_sv.pl
obsolete/cBioPortal_documents.pl 4 additions, 4 deletions

obsolete/cBioPortal_documents.pl
obsolete/parse_svresults.pl 0 additions, 0 deletions

obsolete/parse_svresults.pl
obsolete/somatic_callers.sh 0 additions, 0 deletions

obsolete/somatic_callers.sh
obsolete/svannot.pl 0 additions, 0 deletions

obsolete/svannot.pl
obsolete/uniform_integrated_vcf.pl 0 additions, 0 deletions

obsolete/uniform_integrated_vcf.pl
variants/annotvcf.sh 47 additions, 24 deletions

variants/annotvcf.sh
variants/cnvkit.sh 1 addition, 1 deletion

variants/cnvkit.sh
variants/germline_vc.sh 12 additions, 12 deletions

variants/germline_vc.sh
variants/itdseek.sh 6 additions, 1 deletion

variants/itdseek.sh
variants/pindel.sh 10 additions, 5 deletions

variants/pindel.sh
variants/somatic_vc.sh 6 additions, 5 deletions

variants/somatic_vc.sh
variants/svcalling.sh 12 additions, 8 deletions

variants/svcalling.sh
variants/uni_norm_annot.sh 3 additions, 2 deletions

variants/uni_norm_annot.sh

with 129 additions and 100 deletions

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