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3. GATK Mutect2 "--germline-resource" and "--panel-of-normals" for reference hg19

Thank you both. I converted both files with https://github.com/broadgsa/gatk/blob/master/public/chainFiles/b37tohg19.chain. And GATK Mutect2 ran with no problems. 

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• Manuel Sérgio Sokolov Ravasqueira
• August 06, 2023 09:43
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1. Community
2. General Discussion
3. GetPileupSummaries- Badly formed genome unclippedLoc error - Contig 1 given as location, but this contig isn't present in the Fasta sequence dictionary

Hi Anthony DiCi. I fixed this error by making in my case the -L and -V parameter the same. Can you clarify what changes when this happens?Thanks!

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• Manuel Sérgio Sokolov Ravasqueira
• July 29, 2023 13:36
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1. Community
2. Documentation Questions
3. Converting Reference Genomes from b37 to hg19

I found this: https://github.com/broadgsa/gatk/blob/master/public/chainFiles/b37tohg19.chainHowever this chainfile only has information of chromossome 1 to X and not the mitochondrial and other reg...

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• Manuel Sérgio Sokolov Ravasqueira
• July 28, 2023 16:53
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1. Technical Documentation
2. Glossary
3. Panel of Normals (PON)

Dear GATK team, Thank you for this thread. I want to ask:  I am applying the GATK Mutect2 over TargetSequecing over a set of genes and some genomic regions of interest without having PON of the the...

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• Manuel Sérgio Sokolov Ravasqueira
• July 24, 2023 16:32
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1. Tool Index
2. 4.1.4.1
3. Mutect2

Hello,  In the case of using hg19 human reference, where can I find a panel of normals similar to 1000g_pon.hg38.vcf to pass to this method? Best Regards, Manuel

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• Manuel Sérgio Sokolov Ravasqueira
• July 24, 2023 16:23
• 0 votes