Hello,
I am QC-ing the MJFF genetic data (in bgen format), starting with the samples genotyped on the GSA v5 platform. I’ve used qctool to merge the individual chromosome files and calculate SNP and sample-level summary statistics for filtering. I’m also attempting to estimate sex and compare with reported sex, however I’ve run into problems. Does anyone have advice for checking sex with merged bgen files?
So far I tried the following:
–check-sex argument in PLINK v1.9. This requires bgen v 1.1 input, whereas qctool2 outputs bgen v1.2 by default. When I run the following in qctool2 to filter my merged file to GSA v5 samples only with bgen v1.1 output, it is not recognizing the output file path after the “-og” argument:
$qctool_path -g $scratch_dir/merge_24.bgen -s $samplefile1 -og $scratch_dir/merge_GSAv5_bgen1_1.bgen -incl-samples $samplefile2 -ofiletype bgen_v1.1
!! Error (OptionProcessingException): The following options were not recognised: /scratch/st-silkec-1/project_folders/foxden/samschaf/merge_GSAv5_bgen1_1.bgen…
Installing bgenix to downgrade bgen 1.2 to bgen 1.1 - having an issue with compilation; the compiler cannot find “zlib.”
Using PLINK 2.0 to convert bgen to .ped format, for use with “seXY” inference tool (https://academic.oup.com/bioinformatics/article/33/4/561/2666346).
plink2 --vcf /scratch/st-silkec-1/project_folders/foxden/samschaf/testing/chr1.vcf --recode --out /scratch/st-silkec-1/project_folders/foxden/samschaf/testing/chr1_test_08Jul
Error: Only VCF, oxford, bgen-1.x, haps, hapslegend, A, AD, A-transpose, and
ind-major-bed output have been implemented so far.
As a newbie to genotype processing, I appreciate any input! Thank you.