QC_vis is a tool for quality control report of multiple samples on whole-genome and whole-exome sequencing. It summarises outputs from bioinformatics tools (e.g. FastQC, Picard, GATK) and produces interactive HTML reports for sequencing data interpretation for BigMed project.
PERL5LIB="$PERL5LIB:/where_is_path/QC_vis/lib"
export PERL5LIB
NOTE: we recommend that users add the path of perl libraries to .bashrc, then "source .bashrc"
QC_vis currently accepts outputs from following tools/modules:
- FastQC (outputs from multiple lanes are accepted, and users do not need to merge all lanes per sample before running FastQC)
- Picard (InsertSize, HsMetric, DuplicationMetric and AlignmentSummaryMetric modules)
- GATK (contamination and coverage estimate modules)
- CONPAIR
- FACETS
Users MUST use sample id/name to define the file name of outputs from tools/modules above
Report is generated by running the Perl script create_template.pl, which takes the following arguments and options:
usage: create_template.pl --help [options]
--fastqc path/direcotory [separated by coma, e.g. path1, path2, path3 if multiple paths available] of FASTQC ouputs
--picard path/direcotory [separated by coma, e.g. path1, path2, path3 if multiple paths available] of PICARD ouputs
--gatk path/direcotory [separated by coma, e.g. path1, path2, path3 if multiple paths available] of GATK ouputs
--conpair path/direcotory [separated by coma, e.g. path1, path2, path3 if multiple paths available] of CONPAIR ouputs
--facets path/direcotory [separated by coma, e.g. path1, path2, path3 if multiple paths available] of FACETS ouputs
--control if users would like to report a subset of all samples, please use it for sample control [sample names separated by coma, e.g. name1, name2, name3], and users can also list sample names for controlling in a file
--template directionary of css and javascript used for HTML report
--output output file name
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