==================================================================== `7MMF' `7MF' db MMP""MM""YMM db .M"""bgd `MA ,V P' MM `7 ;MM: ,MI "Y VM: ,V ,6"Yb. `7Mb,od8 `7MM MM ,V^MM. `MMb. MM. M'8) MM MM' "' MM MM ,M `MM `YMMNq. `MM A' ,pm9MM MM MM MM AbmmmqMA . `MM :MM; 8M MM MM MM MM A' VML Mb dM VF `Moo9^Yo..JMML. .JMML. .JMML..AMA. .AMMA.P"Ybmmd" ==================================================================== TODO/ WISHLIST: - Add more verification for BED file input - Remove paired percent chart if data is not paired - Add voting table to report - Sample IDs with a dash in the name do not work (possibly multiple dashes) VariTAS (2020-11-03) v0.0.2 -------------------------------------------------------------- - Removed names from vignettes VariTAS (2020-08-03) v0.0.2 -------------------------------------------------------------- - Added recommended -B parameter to mpileups for Varscan - Vardict now filters out germline variants with an awk command - VarScan now filters out germline variants with an awk command - read.yaml function now exported - Added strand bias filtering to MuTect - Strand bias filtering for MuTect only happens with paired-end data - Added gnomAD to ANNOVAR databases - Removed -d parameter from LoFreq without germline samples (it does nothing) - Added filter that removes duplicated variants from LoFreq output - Temporarily removed -s and -S parameters from LoFreq (mem limit) - LoFreq now runs lofreq viterbi on illumina data - Fixed encoding issue in process.total.coverage.statistics.R in strict latin1 locale VariTAS (2020-02-07) v0.0.1 -------------------------------------------------------------- - Revisions for CRAN submission VariTAS (2019-11-05) v0.8.1 -------------------------------------------------------------- - LoFreq should now call indels - Added dbSNP filtering to LoFreq - Added -s (source quality) parameter to LoFreq, should increase accuracy - Added extra margin to output plots for longer sample names VariTAS (2019-05-06) v0.8.0 -------------------------------------------------------------- - Upgraded to GATK4 throughout pipeline - targetQC step interacts better with job dependencies - Fixed text at bottom of report - Charts now sorted by coverage - Added more CPUs to VarDict commands - MuTect and VarDict should run on ontarget.bam rather than source bam (hybrid) - Fix flagstat with paired normal data - Fix "empty" normal samples appearing in report VariTAS (2019-03-11) v0.7.3 -------------------------------------------------------------- - Fancy new logo - Fixed coverage report bugs - Fixed median coverage plot and adjusted all plot margins - GATK commands updated to work with GATK4 VariTAS (2019-03-01) v0.7.2 -------------------------------------------------------------- - Bugfixes for LoFreq and VarScan - New helper functions to post-process LoFreq and VarScan output - New WIP vignette: What Does This Error Mean? to help with learning how to use VariTAS VariTAS (2019-02-07) v0.7.1 -------------------------------------------------------------- - Added support for LoFreq and VarScan, two matched-normal variant callers VariTAS (2018-12-11) v0.7.0 -------------------------------------------------------------- - Rebranded as VariTAS - New style for plotting coverage by amplicon - Added requirement for gene/feature ID in panel file - Improved compatibility for GRCh38 BCN.AmpliSeq.utilities (2018-11-14) v0.6.3 -------------------------------------------------------------- - Retooled vignettes, now there is only one - Moved example files to inst/extdata - Bugfixes for HPC cross-compatibility BCN.AmpliSeq.utilities (2018-11-09) v0.6.2 -------------------------------------------------------------- - New function run.all.scripts to handle running the pipeline on a non-HPC system - Small changes to other scripts to accomodate this - Added vignette of examples BCN.AmpliSeq.utilities (2018-11-06) v0.6.1 -------------------------------------------------------------- - Updated vignette and description details - Minor bugfix in read.variant.calls - Added read.yaml to helper.functions to remove lab utils package dependency BCN.AmpliSeq.utilities (2018-10-30) v0.6.0 -------------------------------------------------------------- - Added support for single-sample runs in post-processing scripts - Added config option for different HPC systems (LSF [bsub], PBS [qsub], or none) BCN.AmpliSeq.utilities (2018-08-21) v0.5.1 -------------------------------------------------------------- - removed BCN.general.utilities dependency by copying over date.stamp.file.name BCN.AmpliSeq.utilities (2018-08-17) v0.5.0 -------------------------------------------------------------- - removed plotting lib dependency BCN.AmpliSeq.utilities (2018-05-11) v0.4.3 -------------------------------------------------------------- - debugging after coding standard updates - include filters for all variant callers in variant specification in variant Excel sheet - added mean tumour AF column BCN.AmpliSeq.utilities (2018-05-10) v0.4.2 -------------------------------------------------------------- - module load R version in post-processing script BCN.AmpliSeq.utilities (2018-04-27) v0.4.1 -------------------------------------------------------------- - lots of documentation/ minor code updates to comply with package standards BCN.AmpliSeq.utilities (2018-04-26) v0.4.0 -------------------------------------------------------------- - new "mode" option for setting filters - added support for pan-caller specification of variant filters through the "default" filter BCN.AmpliSeq.utilities (2018-04-24) v0.3.4 -------------------------------------------------------------- - added remove_exac filter to remove all ExAC variants at AF>0.01 - new get.gene function to guess gene from panel BCN.AmpliSeq.utilities (2018-04-23) v0.3.3 -------------------------------------------------------------- - bugfixes in run.target.qc function - get.bed.chromosomes: remove header lines starting with "track" - bugfixed vignette BCN.AmpliSeq.utilities (2018-03-08) v0.3.2 -------------------------------------------------------------- - bugfixes to accommodate purely numeric sample IDs BCN.AmpliSeq.utilities (2018-03-08) v0.3.1 -------------------------------------------------------------- - added option for email notification when pipeline finishes - bugfixed reading of MiniSeq sample sheet - new MiniSeq section in vignette BCN.AmpliSeq.utilities (2018-03-01) v0.3.0 -------------------------------------------------------------- - moved all version numbers to config - restructured output to only send PDF report to collaborators by default BCN.AmpliSeq.utilities (2018-02-22) v0.2.6 -------------------------------------------------------------- - added plot of median coverage by amplicon BCN.AmpliSeq.utilities (2018-02-20) v0.2.5 -------------------------------------------------------------- - more plots, and tweaks to existing ones BCN.AmpliSeq.utilities (2018-02-19) v0.2.4 -------------------------------------------------------------- - removed X11 dependency of PDF report BCN.AmpliSeq.utilities (2018-02-16) v0.2.3 -------------------------------------------------------------- - incorporated PDF report BCN.AmpliSeq.utilities (2018-01-29) v0.2.2 -------------------------------------------------------------- - added per sample scatterplots of coverage per amplicon BCN.AmpliSeq.utilities (2018-01-25) v0.2.1 -------------------------------------------------------------- - added prepare.miniseq.specifications to get sample IDs from MiniSeq sample sheet BCN.AmpliSeq.utilities (2018-01-16) v0.2.0 -------------------------------------------------------------- - added run.name argument to accommodate simultaneous running of different datasets with the same sample IDs - new diagnostic plot showing proportion of paired reads BCN.AmpliSeq.utilities (2018-01-15) v0.1.8 -------------------------------------------------------------- - fixed paired-end reads bug BCN.AmpliSeq.utilities (2017-12-14) v0.1.7 -------------------------------------------------------------- - bug fix to accommodate wider range of MiniSeq sample IDs BCN.AmpliSeq.utilities (2017-11-29) v0.1.6 -------------------------------------------------------------- - added variant recurrence plots - changed ontarget percent and mean coverage scatterplots to barplots - fixed a few bugs BCN.AmpliSeq.utilities (2017-11-29) v0.1.5 -------------------------------------------------------------- - more bug fixes - efforts to accommodate isis variant calls BCN.AmpliSeq.utilities (2017-11-28) v0.1.4 -------------------------------------------------------------- - bug fixes - added isis-specific variant annotation script that does not remove biallelic variants BCN.AmpliSeq.utilities (2017-11-24) v0.1.3 -------------------------------------------------------------- - bug fixes and other incremental improvements - implemented isis filters - added coverage by sample plots - added sleep option to post.processing step BCN.AmpliSeq.utilities (2017-11-23) v0.1.2 -------------------------------------------------------------- - more bug fixes - updates to variants per sample barplot to accommodate larger datasets - incorporated target QC as a stage in main pipeline - added run.ampliseq.pipeline.hybrid function BCN.AmpliSeq.utilities (2017-11-22) v0.1.1 -------------------------------------------------------------- - bug fixes BCN.AmpliSeq.utilities (2017-11-22) v0.1.0 -------------------------------------------------------------- - debuting Resources/R version of the package