Hi. I wonder if anyone can direct me to a complete 'truth' SNV set for the 1000genomes NA12878 individual (and, ideally, her mum and dad too). There are a number of existing NA12878 vcf files from various sources, with many or most of the variants in common, but I'm thinking that there must be one 'correct' vcf that the Broad refers to for evaluation etc? The 1000 genomes CEUtrio vcf at ftp://ftp.1000genomes.ebi.ac.uk/vol1...notypes.vcf.gz is a couple of years old now and I'm guessing there's a better call set somewhere. Most particularly I'm after one that is comprehensive, i.e. very few false negatives, as we're looking to evaluate FNR for various sequence depths. Maybe there is one generated from one of these newer very deep sequencing sets for NA12878:
ftp://ftp.1000genomes.ebi.ac.uk/vol1...878/alignment/
which is around 60-70x, and
which look to be ~100x. I think the 1000genomes public VCFs are generated from much earlier GAII based runs?
Any help appreciated
Andrew
ftp://ftp.1000genomes.ebi.ac.uk/vol1...878/alignment/
which is around 60-70x, and
which look to be ~100x. I think the 1000genomes public VCFs are generated from much earlier GAII based runs?
Any help appreciated
Andrew
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