Gold standard variant set
Hi, I want to compare different variant calling pipelines for an exome sample. But, I don't know what gold standard to use for evaluation of performance parameters (sensitivity, specificity, etc). Can anyone suggest me how to create a gold standard for my exome. The genome in a bottle contain gold standard variants for the individual "NA12878" and I presume I cannot use that. Thank you in advance
Regards
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Best Tools and Practices for CNV Variant Calling in WES Data
written by Nadav •
-
CNV benchmarking
written by emma.a •
-
Benchmark dataset of low confidence variants
written by mera El •
-
Validation of somatic variant calling pipeline
written by Elisa •
-
Gold standard for Mitochondrial DNA variant calling
written by Anh •
-
News: precisionFDA is launching the Truth Challenge V2: Calling Variants from Short and Long Reads …
written by stephens_sarah
-
Basic difference between haplotype variant callers
written by sofie_carolina •
-
Is there gold standard data for ancestral reconstruction?
written by c_u
-
Comparing two VCFs and drawing a precision-recall curve
written by eric.kai0918 •
-
Troubles comparing SNP called on Illumina reference human genome
written by wpierrick •
Meaning you have sequenced a specific sample and want to compare pipelines?
By the way, while this might be interesting for you, this has been done hundreds of times. For a recent good comparison see this paper.
Yes, i have sequenced my sample and want to compare pipelines. Thank you for suggesting this reference paper. Is there any more studies describing the process of generating a gold standard dataset for our sample? Thanks
You cannot create a ground truth set without an orthogonal technique.
Why do you want to create your own gold standard? The thing about gold standards is that you only make one of them, since they're a lot of work.