Releases: patidarr/ngs_pipeline
Stable Release 2.9
Added cnvkit for clinomics capture kits.
conpair for contamination estimation
featurecount for TMM
do mpileup on hotspot positions +-5
if split fastq files are available merge them in workdir/ make links if single fastq files
parse snakemake stats to human readable format
Stable Release 2.8
HLA Typing on all bam files
Fix bug in uniq sort wherever used
added whitelisted bed region file
Merged ProteinCoding.pl and Filter.pl to one script
Added circos on RNASeq only ==> last fix created this issue
Added Bed file for NIAID Libraries
use sbatchT, access full result of jobhist
Stable Release 2.7
HLA Typing/Neoantigen Prediction is mature enough to be considered in Stable release.
Novoalign/bma2mpg removed from this version
Bismark mapping is included.
v2.6
stable release Feb2017
Failed Exon input is filtered on mapping quality.
stable release Jan2017
Added Sequenza, VerifyBamID, Actionable Rule Changes, Cluster Resources
stable release 2.3
Added STAR, subread for FPKM calculation
Sequenza for copy number
Other functionalities like final email is correct, no consolidated file on all samples, successful file is not available if pipeline is running.
Stable Release for clinomics
v2.2 v2.2
Last version using PBS on TGen
v2.1 better onerror
stable release 2.0
This version included some of the major changes:
1 similar bed file format for all capture types
2 hotspot bed files based on capture method
3 GTF file updates to latest version
4 Exon bed files updates to latest version
5 annotation pipeline rewrote as rules
6 biowulf resources optimization for various tools
7 cufflinks fix (do not check for new version)
8 remove panels from circos plot etc...