megSAP - DNA analysis (multi-sample and trio)
June 22, 2026 ยท View on GitHub
Prerequisite: Single sample analysis
The multi-sample and trio pipelines require files form the sinlge sample analysis (BAM, VCF, ...).
Thus, each samples has to be analyzed using the single sample analysis first.
After the single-sample analyses, the multi-sample or trio analysis is perfomed.
Multi-sample pipeline
Basics
Multi-sample DNA analysis is performed using the multisample_longread.php script.
Please have a look at the help using:
> php megSAP/src/Pipelines/multisample_longread.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 INI file.
Note: The processing system of the first sample is used to determine the target region for the multi-sample and trio analyses.
Output
After the analysis, these files are created in the output folder:
- small variants VCF/GSvar file
- CNV TSV file
- structural variants VCF/BEDPE file
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_longread.php script.
Please have a look at the help using:
> php megSAP/src/Pipelines/trio_longread.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 INI file.
Output
The same files as in the multi-sample analysis are produced.