Ahmet Sayici

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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• 16 February 2026 08:24
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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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• 02 February 2026 14:48
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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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• Edited 14 January 2026 10:00
• 1 vote

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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• Edited 11 December 2025 10:53
• 1 vote

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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• 09 December 2025 15:46
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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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• 14 November 2025 13:29
• 1 vote