1. Getting Started
2. FAQ
3. Which training sets arguments should I use for running VQSR?

Dear development team,  I found a VQSR parameter discrepancy for omni dataset usage. Some previous GATK3 posts and this post indicate the setting for omni  as below --resource:omni,known=false,trai...

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• Jacob Shujui Hsu
• July 12, 2021 03:16
• 3 votes

1. Tool Index
2. 4.2.0.0
3. VariantRecalibrator

I can confirm that the links for VQSR are still missed (May 2021).  Also, I found a VQSR parameter discrepancy for omni dataset usage. Some previous GATK3 posts indicate the setting for omni and he...

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• Jacob Shujui Hsu
• May 03, 2021 04:35
• Edited
• 1 vote

1. Technical Documentation
2. Algorithms
3. Variant Quality Score Recalibration (VQSR)

I can confirm that the links for VQSR are still missed (May 2021).  Also, I found a VQSR parameter discrepancy for omni dataset usage. Some previous GATK3 posts indicate the setting for omni datase...

• View comment
• Jacob Shujui Hsu
• May 03, 2021 04:36
• Edited
• 0 votes

1. Tool Index
2. 4.1.8.1
3. VariantRecalibrator

I can confime that the links for VQSR are still missed (May 2021).  Also, I found a VQSR parameter discrepancy for omni dataset usage. Above post indicate the setting from 3.8 and here  --resource:...

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• Jacob Shujui Hsu
• May 03, 2021 04:30
• Edited
• 0 votes

1. Technical Documentation
2. Glossary
3. GVCF - Genomic Variant Call Format

How to determine if there is a missing position? Is this the only case? GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0

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• Jacob Shujui Hsu
• March 27, 2021 10:36
• 0 votes