Ahmet Sayici
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Latest activity by Ahmet Sayici
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Ahmet Sayici commented,
I use PVAR files under `DRAGEN population level WGS variants, PLINK format [500k release]`. They are per chromosome. You can still find the FILTER column in those PVAR files.
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Ahmet Sayici commented,
You can use the new ML-Corrected DRAGEN PVAR files. They have a column of FILTER. You can create either an exclude or an extract file by setting FILTER!=PASS or FILTER==PASS respectively.
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Ahmet Sayici commented,
If you run your jobs using Low priority, it is likely that your jobs fail with SpotInstanceInterruption and wait for another spot instance indefinitely. I recommend to run them at least using Norma...
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Ahmet Sayici commented,
Hi Francesco,In this case I would use PLINK2 with Bulk/DRAGEN WGS/DRAGEN population level WGS variants, PLINK format [500k release] in a ttyd instance. Bigger the ttyd, faster the analyses. There i...
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Ahmet Sayici commented,
New ML-Corrected DRAGEN whole genome sequencing (WGS) release makes everything so easy. Just go to Bulk/DRAGEN WGS/DRAGEN population level WGS variants, PLINK format [500k release] and check .pvar ...
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Ahmet Sayici commented,
Unfortunately, compiling doesn't work for me too. So I started to use pre-built bgenix. You can download it directly from their website http://www.well.ox.ac.uk/~gav/resources/
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Ahmet Sayici created a post,
WGS BGEN files are ref-last.
Hi,I am currently working with whole-genome sequencing (WGS) data and performing rare variant collapsing tests using REGENIE. Initially, I used the --ref-first parameter, assuming the BGEN files fo...
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