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megSAP - DNA analysis (single sample)

Basics

Single sample DNA analysis is performed using the analyze.php script.
Please have a look at the help using:

> php megSAP/src/Pipelines/analyze.php --help

The main parameters that you have to provide are:

  • folder - The sample folder, which contains the the FASTQ files as produced by bcl2fastq2.
  • name - The sample name, which must be a prefix of the FASTQ files.
  • steps - Analysis steps to perform. Please use ma,vc to perform mapping and variant calling (with annotation).
  • system - The processing system INI file.

Poster

A poster about megSAP which describes the all steps of the single-sample analysis pipeline can be found here.

Running an analysis

The analysis pipeline assumes that that all data to analyze resides in a sample folder as produced by Illumina's bcl2fastq tool. If that is the case, the whole analysis is performed with one command, for example like this:

php megSAP/src/Pipelines/analyze.php -folder Sample_NA12878_01 -name NA12878_01 -system hpHBOCv5.ini -steps ma,vc

In the example above, the configuration of the pipeline is done using the hpHBOCv5.ini file, which contains all necessary information (see processing system INI file).

Running an analysis with DRAGEN

A short instruction how to setup the DRAGEN can be found here. To run an analysis with DRAGEN mapping you simply has to pass the parameter -use_dragen to the analysis.php:

php megSAP/src/Pipelines/analyze.php -folder Sample_NA12878_01 -name NA12878_01 -system hpHBOCv5.ini -steps ma,vc -use_dragen

Performance

A performance comparison between the megSAP pipeline using DRAGEN vs. bwa can be found here

Test data

Example data which can be analyzed using the command above can be downloaded from here.

Output

After the analysis, these files are created in the output folder:

  1. mapped reads in BAM format
  2. a variant list in VCF format
  3. a variant list in GSvar format
  4. QC data in qcML format, which can be opened with a web browser

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