unify chromosome representation to hg19 style (chr1-chr22,chrX,chrY,chrM)
- especially for chrX,chrY,chrM
New function: link_l() - takes list of regular expressions
added function (link_l()) to process list of file patterns
added argument ('RSQ',default=F) to handle both RNASeq & WXS in one function
parameter update
added parameters to control memory, #cpu for mutect run
minor change to run RNAseq samples from SGI
minor change to run RNAseq samples from SGI
no need to run FastQC every time of pipeline run. One batch run at the beginning of analysis is enough.
Omitting fastqc from rsq2mut pipeline.
minor change to process SGI samples
Routines to process output from VEP
added argument (normalL=[]) to functions link() & link_l() to distinguish normal from tumor samples
- WXS files are assumed from SureSelect (S*_[TB]_SS.[12].fq.gz)
minor typo correction
javascript modified to handle pair id whose length is not 4('S' + 3 digit).
Made RNA-Seq pipeline scripts refer to the 'storageBase','apacheBase' in 'mypipe' package.
Added arguments to pipeline: server(smc1 or smc2), genome(hg18 or hg19)
: to be free from actual configuration of server
collect RNA-seq sample from rpkm_gene_expr table
don't check deletions in cosmic db preparation
modifications due to new data
changes due to new SGI data (20131031)
copy index files for bam