Compare Allelic Frequency to Ground truth
Entering edit mode
5.0 years ago
ingalemme • 0

Hi everyone,

I try to compare two different variant caller (one is the GATK MuTect2 pipeline). For this I want to compare the allelic frequency of the called variants from both pipelines to a ground truth. I know that for example 'horizon' provides samples which can be used for sequencing which have variants with a given allelic frequency. But for this I need to do all the sequencing. I am looking for a fastq file (with known variants and allelic frequencys - preferable as vcf) which I can feed to my two pipelines. So far I only found true data (vcf and fastq) which allow me to tell whether I have TP, NP, etc but not whether the frequencies are as expected. I know I could simulate reads by myself but this comparison is only supposed to give me a quick overview.

I would appreciate your help very much and I hope you did understand my question! XD

Thank you!!!!

GATK fastQ VariantCalling Raw Data Ground truth • 960 views

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