I initially uploaded F999912 only with FTDNA SNPs. Surprised with lots of matches, I then uploaded F999913 but with SNPs tested by all DNA companies and removed the previous kit. Both kits were from VCF files provided by the authors used in their experiment where Clovis Anzick sample is one of the genotype (second) among other samples used for comparison.
The bad news is, I am not sure if those SNPs were the complete set or some sort of filtered version used for their experiment. The good news is, we have the BAM files and the sequence reads available. However, their size is enormous and takes ages to process them. I began processing last week and still it seems to take another week, but chromosome 3 is complete.
I am grateful for the owner of kit# F334678 (Robin Frisella) who sent me her autosomal file for SNP by SNP comparison and allowed me to post the results.
There are several segments matching with no errors at 5 cM / 500 SNPs. However, I will take the first segment match, chromosome 3 as I now have the SNPs of Clovis Anzick not only from VCF (F999913), but also from the BAM file.
A detailed SNP-by-SNP comparision : Clovis-Anzick-Segment-Analysis.xlsx
Based on the SNP by SNP analysis, for a matching segment from kit# F334678, it not only showed the segment match is so real with no errors (sites where F999913 had no-calls), the Clovis Anzick sample processed from BAM file had significantly more SNPs that are common with DNA testing companies. Hence, the VCFs contained only some filtered SNPs used by authors in their experiment and BAM files contains all SNPs. The BAM processing for Clovis Anzick is not yet complete and it will take atleast another week. Once processed, I will replace kit# F999913 which will give more accurate results/matches with no-calls issue for Clovis Anzick. I will try to retain the same kit number if possible.
The bad news is, I am not sure if those SNPs were the complete set or some sort of filtered version used for their experiment. The good news is, we have the BAM files and the sequence reads available. However, their size is enormous and takes ages to process them. I began processing last week and still it seems to take another week, but chromosome 3 is complete.
I am grateful for the owner of kit# F334678 (Robin Frisella) who sent me her autosomal file for SNP by SNP comparison and allowed me to post the results.
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| GEDMatch 1-to-1 comparision |
A detailed SNP-by-SNP comparision : Clovis-Anzick-Segment-Analysis.xlsx
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| Preview of SNP by SNP Analysis |