dna_multi_sample.md

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).

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 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).

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.

back to the start page