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megSAP - DNA analysis (multi-sample and trio)

Multi-sample pipeline

Basics

Multi-sample DNA analysis is performed using the multisample.php script.
Please have a look at the help using:

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

The main parameters that you have to provide are:

  • bams - A list of input BAM files.
  • status - A comma-separated list of affected status corresponding to the input BAM files.
  • out_folder - Output folder.
  • system - The processing system configuration INI file (see next section).

Note: The processing system of the first sample is used to determine the target region for the multi-sample and trio analyses.

Tools used in this analysis pipeline

Mapping is not part of this pipline - it has to be perfomed beforehand using the single-sample pipeline. The tools used for variant calling and annotation are the same as for the single-sample pipeline.

Output

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

  1. a multi-sample variant list all.vcf.gz in VCF format.
  2. a multi-sample variant list multi.GSvar in GSvar format.

Trio pipeline

Basics

Trio DNA analysis is a special case of the multi-sample analysis for an affected child and healthy parents.
It is performed using the trio.php script.
Please have a look at the help using:

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

The main parameters that you have to provide are:

  • f - BAM file of father.
  • m - BAM file of mother.
  • c - BAM file of child (index).
  • out_folder - Output folder.
  • system - The processing system configuration INI file (see next section).

Tools used in this analysis pipeline

Mapping is not part of this pipline - it has to be perfomed beforehand using the single-sample pipeline. The tools used for variant calling and annotation are the same as for the single-sample pipeline.

Output

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

  1. a multi-sample variant list all.vcf.gz in VCF format.
  2. a multi-sample variant list trio.GSvar in GSvar format.

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