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dna_tumor-normal_pair.md

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megSAP - DNA analysis (tumor/normal pairs)

Analysis pipeline

Somatic analysis of tumor/normal DNA sample pairs is performed with somatic_dna.php.

Mapping single samples

The somatic pipeline requires tumor and normal sample BAM files.
Thus, they need to be mapped first using the analysis.php with the parameter -steps ma -somatic.
For more information, see the documentation at single sample DNA analysis.

Somatic variant calling (tumor/normal)

After mapping, the tumor and normal BAM files are used to perform somatic variant calling.

The main parameters that you have to provide are:

  • t_bam - the tumor DNA sample BAM file
  • n_bam - the normal DNA sample BAM file (only required for tumor/normal analysis)
  • -out_folder - the output folder

Please have a look at the help:

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

Tools used in this analysis pipeline

The tools used in this analysis can be found here: Somatic tools.

Performance

Performance benchmarks of the the megSAP pipeline can be found here.

Output

The main output files are listed below.

Variant calling step (vc, an):

  • somatic_var.vcf.gz - SNVs and short indels called with Strelka2 (sample pairs) or FreeBayes (tumor sample only)
  • somatic_var_annotated.vcf.gz and somatic.GSvar - annotated variants
  • somatic_var_structural.vcf.gz and somatic_var_structural.tsv - structural variants called with manta
  • somatic_bafs.igv - B-allele frequencies in IGV-compatible tabular format

Copy-number variation calling step (cn):

  • somatic_clincnv.tsv - copy-number variations called with ClinCNV

Microsatellite analysis step (msi):

  • somatic_msi.tsv - microsatellite instabilities called with MANTIS

Additional annotation steps

RNA annotation (an_rna): If you have data from the RNA pipeline, this data can be annotated in the an_rna step. This will annotate read depth, allele frequency and TPM from the RNA sample to each variant contained in the GSvar file. Provide the bam file using the parameter -t_rna_bam and the RNA sample name using the parameter -rna_id. This step also annotates reference gene expression from The Human Protein Atlas. Therefore, you have to specify a reference tissue type. It can be passed via the parameter -rna_ref_tissue.

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