1. Tool Index
2. 4.1.8.1
3. VariantRecalibrator

Hi all, *Hope everyone is okay* I need some help here, with VQSR command recomendations. I've read this documentation and soon we will try to run VQSR steps (on latest GATK version). I'm using GATK...

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• Monete Rajão Gomes
• August 14, 2020 20:15
• Edited
• 0 votes

1. Tool Index
2. 4.1.7.0
3. HaplotypeCaller

Hi Devendra Waikul Unfortunately, I've never used genomicsDBImport before. I've been using combinegvcf, instead. Maybe you should look for this error in other sites or in read-only GATK v3 previous...

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• Monete Rajão Gomes
• June 25, 2020 18:07
• Edited
• 0 votes

1. Tool Index
2. 4.1.7.0
3. HaplotypeCaller

Hi Devendra,   I think when you use -ERC GVCF option, your output should be "output_haplotype.g.vcf" or (better) "output_haplotype.g.vcf.gz" Like described above on session: Single-sample GVCF call...

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• Monete Rajão Gomes
• June 23, 2020 17:37
• Edited
• 0 votes

1. Getting Started
2. FAQ
3. Where can I find known variants, training and truth sets, and other resource files?

Hi, I have some doubts and I hope anyone could help me. I'm trying to run gatk pipeline again (I did before successfully), and I decided to use as known site, dbSNP last release (v153). So, I've do...

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• Monete Rajão Gomes
• April 17, 2020 21:14
• 1 vote