Somatic truth set

Does anyone know if there is a somatic truth set vcf available? I know there are now several available for germline samples from GIAB

I read this paper Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection but it looks as though they don't provide the actual vcf truthset to compare against locally.

The paper also points to the Bamsurgeon tool it looks like you can generate your own variants for a given bam but I'm wanting to simulate a somatic panel so the depth would be 500-1000 (I don't know where you would get a bam of that depth for human unless it's a panel)

benchmarking somatic

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updated 3.4 years ago by lethalfang •

• written 3.4 years ago by samuel

1 answer

I think I have found an naswer to my own question. Should anyone have the same question as of March 2023 the relevant data and information can be found here:

WGS/WES:

Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing

Panels: A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency

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written 3.4 years ago by samuel

Just in case things are hard to find, for the WGS/WES, these are the data (what the file names mean: https://sites.google.com/view/seqc2/home/sequencing): https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/data/

These are the vcf's: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/release/latest/

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written 3.4 years ago by lethalfang •