Hi
I have run -snp-stats on a 1000Genomes imputed set of bgen files. In the case of 3 chromosomes, the number of variants in the snp-stats output is one less than the reported number of variants in the file (as reported by qctools during processing). Based on my investigations so far, I think this is because there is a duplicate variant in the bgen files, that is two variants with the same chr:bp identity and the same alleles. I am just wondering how qctools is programmed to deal with duplications like this? And has this changed over time? Only I have some summary stats that were generated for the same dataset a few years ago and in these files, the duplicate appears twice (see below) with slightly different stats, hence why I suspect this is the source of the mismatch in variant number this time around (as this variant only appears in the new snp-stats output once).
SNPID RSID chromosome position A_allele B_allele minor_allele major_allele
19:48773401 19:48773401 19 48773401 C <DEL> <DEL> C
19:48773401 19:48773401 19 48773401 C <DEL> <DEL> C
Would be great to get some feedback on this!
Thanks
Laura
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