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apriha / snps

tools for reading, writing, merging, and remapping SNPs
BSD 3-Clause "New" or "Revised" License
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Inconsistent output of mitochondrial SNPs in Ancestry/23andme merge #65

Closed GerardManning closed 4 years ago

GerardManning commented 4 years ago

Ancestry reports mitochondrial (MT/Chr26) SNPs as diploid (e.g. "GG", with two identical alleles), even though there is just one mitochondrial genome, with multiple copies. 23andme reports as haploid (e.g. "G"). When 23andme and Ancestry files are merged in lineage, the csv output has a single allele for all 23andme SNPs but two alleles for any that are present on Ancestry (including SNPs present on both).

Suggest that, for consistency, all MT SNPs be reported with a single allele, and any heterozygosity in Ancestry calls (due to heteroplasmy, which I've never yet seen) be reported as an error.

apriha commented 4 years ago

Like deduplicate_XY_chrom, this could be addressed in a similar manner with deduplicate_MT_chrom (new parameter to SNPs).