To validate somatic variant calling, we simulate tumor samples with different tumor content by mixing two germline samples in different ratios.
We selected NA12878 and NA12877 because gold-standard variant lists are available for the samples (NA12878 / NA12877).  NA12878 and NA12877 were sequenced using the IMGAG Twist custom exome V2 (Twist Core, Twist RefSeq, Twist Mito and custom content).  For the benchmark, we evaluated sensitivity/specificity for different AF cutoffs on the benchmark region.  The benchmark region is the intersection of kit target region, NA12878 high-confidence region, NA12877 high-confidence region and tumor/normal high-coverage region above 60x).   The original .bam files were provided by Marc Sturm from the Institut f?r Medizinische Genetik und Angewandte Genomik at the University Clinic T?bingen, see https://download.imgag.de/public/validation_dataset_somatic/readme.html.  The files were transformed into .fastq.gz files using the nf-core/bamtofastq pipeline with Nextflow 23.10.1: nextflow run nf-core/bamtofastq -profile cfc -r 2.1.0 --input bam-to-fastq/bam2fastq_samplesheet.csv --outdir bam-to-fastq/
We selected NA12878 and NA12877 because gold-standard variant lists are available for the samples (NA12878 / NA12877).  NA12878 and NA12877 were sequenced using the IMGAG Twist custom exome V2 (Twist Core, Twist RefSeq, Twist Mito and custom content).  For the benchmark, we evaluated sensitivity/specificity for different AF cutoffs on the benchmark region.  The benchmark region is the intersection of kit target region, NA12878 high-confidence region, NA12877 high-confidence region and tumor/normal high-coverage region above 60x).   The original .bam files were provided by Marc Sturm from the Institut f?r Medizinische Genetik und Angewandte Genomik at the University Clinic T?bingen, see https://download.imgag.de/public/validation_dataset_somatic/readme.html.  The files were transformed into .fastq.gz files using the nf-core/bamtofastq pipeline with Nextflow 23.10.1: nextflow run nf-core/bamtofastq -profile cfc -r 2.1.0 --input bam-to-fastq/bam2fastq_samplesheet.csv --outdir bam-to-fastq/