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dna_tumor-normal_pair.md

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megSAP - DNA analysis (tumor-normal pair)

Basics

Tumor-normal pairs can be analyzed by using the somatic_dna.php script. This script is also used by several project specific data analysis pipelines. For example, the script somatic_emed.php can be used for analysis of combined DNA/RNA tumor-normal data.

Please also look at the help using:

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

The main parameters that you have to provide are:

  • p_folder - Project folder that contains all sample folders that will be used for the current analysis. The sample folders should be named like Sample_ID while ID is the corresponding sample ID. Sample IDs are given by the parameters t_id and n_id. Sample folders contain the FASTQ files produced by bcl2fastq2.
  • t_id - The tumor sample name, which must be a prefix of the FASTQ files.
  • n_id - The normal sample name, which must be a prefix of the FASTQ files.
  • o_folder - The output folder.
  • steps - Analysis steps to perform. Please use ma,vc,an to perform mapping, variant calling and variant annotation.
  • filter_set - Filter set to use for post-call variant filtering. Applies only if annotation step is selected. Multiple filters can be comma separated. Same options like in filter_vcf.php
  • min_af - Minimum variant allele frequency to detect.
  • t_sys - The processing system INI file for the tumor sample.
  • n_sys - The processing system INI file for the normal sample.
  • nsc - Skip sample correlation check. This is useful if sample correlation is low and the pipeline will give an error otherwise.

Output

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