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weizhouUMICH / SAIGE

GNU Lesser General Public License v3.0
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Error: No queried variant is found in the bgen file #206

Closed Qiaolan closed 4 years ago

Qiaolan commented 4 years ago

Hi @weizhouUMICH ,

I saw your new paper, congratulations!

I get the error below in the step 2 of saige gene-based:

geneID: SLC37A1 [1] "SLC37A1 \t21:43959666\t21:43959714" genetic variants with 6.052829e-06 <= MAF <= 0.5 are included for gene-based tests [1] "ids_to_include" [1] "21:43959666" "21:43959714" TEST 2 TEST 1 OK TEST2 2 ranges_to_include.nrow() 0 ranges_to_exclude.nrow() 0 ids_to_include.size() 2 ids_to_exclude.size() 0 No queried variant is found in the bgen file! All variants bgen file will be analyzed Mtest: 0 closed the genofile! cntMarker: 0 [1] "No samples are left after removing samples with missing dosages/genotypes of variants in the gene" closed the genofile!

However, snp 21:43959666 is actually in my bgen file:

-bash-4.2$ grep 21:43959666 * Binary file ega_exome_chr21.bgen matches Binary file ega_exome_chr21.bgen.bgi matches ega_exome_chr21.bim:21 21:43959666:G:A 0 43959666 A G

Do you know why I got this error? Thanks!

Ojami commented 4 years ago

Just a thought: min/maj alleles missing? e.g. it is supposed to be in the following format:

SLC37A1 21:43959666_G/A

Best/Oveis