Chromosomes in bim file are not in ascending order.

pjgreer / ukb-rap-tools

Scripts and workflows for use analyzing UK Biobank data from the DNANexus Research Analysis Platform

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Chromosomes in bim file are not in ascending order. #20

Open frahimov opened 1 month ago

frahimov commented 1 month ago

Hi, I was able to use your scripts to prepare input files, including liftover. Although, at one point I had to change the instance memory from mem1_ssd1_v2_x16 to mem2_ssd1_v2_x48, because the instance ran out of memory during liftover.

But at regenie step 1 I got this error. Have you seen this error?

bim : [ukb22418_autosomeQC_c1_22_mrg_prnd_cohort_lo38_v3.bim] ERROR: chromosomes in bim file are not in ascending order.

I included only autosomal variants for Step 1.

pjgreer commented 2 weeks ago

What step was this?

Did gt prep step 1 run completely and then this error was in step 2, or weas this all in step 1?

This happens then the merge-list order gets messed up. One way to fix is to read in the bed file and export it again. I haven't seen this happen before in the gt prep files. so may have to do some more digging.