The mapping pipeline has been created for NGS users who want to align there data with the most commonly used alignment programs. The pipeline performs a quality control (QC) on the raw fastq files with our Flexiprep pipeline. After the QC, the pipeline simply maps the reads with the chosen aligner. The resulting BAM files will be sorted on coordinates and indexed, for downstream analysis.

Tools for this pipeline:


Note that one should first create the appropriate configs.

For the help menu:

java -jar </path/to/biopet.jar> pipeline mapping -h

Arguments for Mapping:
 -R1,--input_r1 <input_r1>                       R1 fastq file
 -outDir,--output_directory <output_directory>   Output directory
 -R2,--input_r2 <input_r2>                       R2 fastq file
 -outputName,--outputname <outputname>           Output name
 -skipflexiprep,--skipflexiprep                  Skip flexiprep
 -skipmarkduplicates,--skipmarkduplicates        Skip mark duplicates
 -skipmetrics,--skipmetrics                      Skip metrics
 -ALN,--aligner <aligner>                        Aligner
 -R,--reference <reference>                      Reference
 -chunking,--chunking                            Chunking
 -numberChunks,--numberchunks <numberchunks>     Number of chunks, if not defined pipeline will automatically calculate the number of chunks
 -RGID,--rgid <rgid>                             Readgroup ID
 -RGLB,--rglb <rglb>                             Readgroup Library
 -RGPL,--rgpl <rgpl>                             Readgroup Platform
 -RGPU,--rgpu <rgpu>                             Readgroup platform unit
 -RGSM,--rgsm <rgsm>                             Readgroup sample
 -RGCN,--rgcn <rgcn>                             Readgroup sequencing center
 -RGDS,--rgds <rgds>                             Readgroup description
 -RGDT,--rgdt <rgdt>                             Readgroup sequencing date
 -RGPI,--rgpi <rgpi>                             Readgroup predicted insert size
 -config,--config_file <config_file>             JSON config file(s)
 -DSC,--disablescatterdefault                    Disable all scatters

To run the pipeline:

java -jar </path/to/biopet.jar> pipeline mapping -run --config mySettings.json \
-R1 myReads1.fastq -R2 myReads2.fastq -outDir myOutDir -OutputName myReadsOutput \
-R hg19.fasta -RGSM mySampleName -RGLB myLib1

Note that removing -R2 causes the pipeline to be able of handlind single end .fastq files.

To perform a dry run simply remove -run from the commandline call.

Result files

├── OutDir
    ├── <samplename>-lib_1.dedup.bai
    ├── <samplename>-lib_1.dedup.bam
    ├── <samplename>-lib_1.dedup.metrics
    ├── flexiprep
    └── metrics