GIAB Truth Set

Question

[samuel]

Hi,

Does anyone know what coverage the GIAB truth set is for NA12878?

I was wanting to download the vcf from here GIAB truthset vcf but it would be good to know what the mean coverage is.

I have read this paper Best practices for benchmarking germline small-variant calls in human genomes and this paper Extensive sequencing of seven human genomes to characterize benchmark reference materials but I can't seem to find the info anywhere.

Answer 1

[Jeremy Leipzig]

The truthset is an amalgam or consensus of at least 3 different sequencing technologies (Complete Genomics, 10X, Illumina). I'm not sure coverage is easily interpretable.

In spot checking at the HG002_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-Solid-10X_CHROM1-22_v3.3_highconf.vcf.gz VCF itself, the depth is usually over 300X.

[samuel]

Thanks Jeremy