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README.md
collapse_speedseq_regions.snakefile
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somatic_concordance-config.yaml
somatic_concordance.snakefile

README.md

Somatic truth sets from Genome in a Bottle samples

A mixture of two Genome in a Bottle samples -- NA12878 and NA24385 -- to emulate a somatic-like tumor-normal set. Known calls from these two samples can be used to estimate true and false positives from somatic variant callers. Input BAMs and a complete description of the experimental setup are available from the Genome in a Bottle FTP site:

ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/use_cases/mixtures/UMCUTRECHT_NA12878_NA24385_mixture_10052016/

giab_truthset.snakefile has the full commands for creating the truth sets.

NA12878 and NA24385 are from Genome in a Bottle v3.3.2 calls.

The somatic truth sets contain two annotations:

  • FREQ: Specifying the expected frequency of the mutation: 30% and 15% for NA12878 homozygotes and heterozygotes from the 30% NA12878 70% NA24385 tumor-like mixture.
  • SOMTYPE: A classification for the somatic type (high_freq_somatic and mod_freq_somatic) useful in training.

Build 37

Build 38