rjsicko
commented
6 years ago PAR coordinates for GRCh37.p13 in case it helps when adjusting filter.
Name | Chr | Start | Stop PAR#1 | X | 60,001 | 2,699,520 PAR#2 | X | 154,931,044 | 155,260,560 PAR#1 | Y | 10,001 | 2,649,520 PAR#2 | Y | 59,034,050 | 59,363,566
I think the warning "This means that the site is covered in fewer than 80% of the individuals in ExAC, which may indicate a low-quality site." is not account for male/female status in AC.
example variant with the warning
rational for why I think that filter isn't accounting for male/female:
Number of individuals in ExAC 33,644 - male 27,062 - female 60,706 – total
So, there should be 87,768 alleles for an X chr SNP not in the PAR.
For the 80% individuals cutoff we can have the two extremes: 48,564 individuals – 33,644 males = 14,920 females -> 63,484 alleles as a cutoff for 80% individuals (if all the 20% fails are female)
48,564 individuals – 27,062 females = 21,502 males -> 75,626 alleles as a cutoff for 80% individuals (if all the 20% fails are male)
edit: related issue reported in gnomad repo.
line 175 of 4b9e607 exac_browser/templates/variant.html line 428 of 07d003b gnomad_browser/templates/variant.html (commented out)
{% if variant.allele_num < 97129.6 %}