I am contacting you because I have found discrepancies with the 1000 genomes project. I have been using the database to see the variation in human populations. But I have found sites where not exist variation in the 1000 genomes project and these differ with gnomAD.
For example, rs113875178 where the alleles are A/C (A is the reference). This site is not found in the VCF file, so I am assuming that 100% of the population doesn´t have variation (it has not been called in the 1000 genomes project and the reference allele are present at that position). But in gnomAD the ALT genotype is the majority (C).
What happen with these kinds of snp? Did the 1000 genomes project not be considered? I don´t know if my interpretation is wrong, errors by reassignment, I'm missing some data that I'm not observing, reads with errors or missing information on the page. Do you used the reads of 1000 genomes or the vcf file?.
I hope you could help me with my doubts.
Thank you for your help
I am contacting you because I have found discrepancies with the 1000 genomes project. I have been using the database to see the variation in human populations. But I have found sites where not exist variation in the 1000 genomes project and these differ with gnomAD.
For example, rs113875178 where the alleles are A/C (A is the reference). This site is not found in the VCF file, so I am assuming that 100% of the population doesn´t have variation (it has not been called in the 1000 genomes project and the reference allele are present at that position). But in gnomAD the ALT genotype is the majority (C).
What happen with these kinds of snp? Did the 1000 genomes project not be considered? I don´t know if my interpretation is wrong, errors by reassignment, I'm missing some data that I'm not observing, reads with errors or missing information on the page. Do you used the reads of 1000 genomes or the vcf file?.
I hope you could help me with my doubts. Thank you for your help