Update docs/SOMATIC_SNV_BENCHMARK.md

Co-authored-by: Dan Miller <dmiller15@users.noreply.github.com>
kids-first · Jun 28, 2024 · a423d9e · a423d9e
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diff --git a/docs/SOMATIC_SNV_BENCHMARK.md b/docs/SOMATIC_SNV_BENCHMARK.md
@@ -13,12 +13,12 @@ BAM files relevant to our workflow (BWA-aligned) were called using our standard
 1. Gold standard VCFs were downloaded from https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/release/v1.2/ with [SNV](https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/release/v1.2/sSNV.MSDUKT.superSet.v1.2.vcf.gz) and [INDEL](https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/release/v1.2/sINDEL.MDKT.superSet.v1.2.vcf.gz) VCFs merged into a single VCF
 1. Merged gold standard VCF was then subset to BWA hits and broken up into call sets matching samples (parse `calledSamples` `INFO` field)
 1. Next, a custom [benchmark script](https://github.com/kids-first/kfdrc-benchmark/blob/main/scripts/benchmark_vcf_calls.py), which collected the following metrics:
- - True Positive
- - False Positive
- - False Negative
- - F1 Score
- - Precision
- - Accuracy
+   - True Positive
+   - False Positive
+   - False Negative
+   - F1 Score
+   - Precision
+   - Accuracy
 
 ## Cell Line Consensus Call Method Benchmarking Results
  Results were collated into the following tables, broken down by confidence level aggregations for the cell line data: