1. Community
2. Somatic

Hi, I am running a Somatic variant discovery protocol on plant samples.Currently at the GetPileupSummaries stage. This stage requires a common germline variant sites VCF file.However, there is no s...

• Arye Harel
• November 15, 2022 15:54
• Edited
• 2 followers
• 4 comments
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1. Community
2. Special GATK Use Cases

Regarding the "Somatic short variant discovery" pipeline (https://gatk.broadinstitute.org/hc/en-us/articles/360035894731). Since this pipeline  allows identifying INDELS, is it the correct protocol...

• Arye Harel
• June 23, 2022 11:41
• 2 followers
• 6 comments
• 0 votes

1. Community
2. General Discussion

REQUIRED for all errors and issues: a) GATK version used: gatk4-v4.1.9.0 (Can use also gatk3-v3.8.0)b) Exact command used: NAc) Entire program log: NA Hi, Which protocol should be used for microsat...

• Arye Harel
• June 15, 2022 08:27
• Edited
• 3 followers
• 5 comments
• 0 votes

1. Community
2. Germline

a)How do I work with large data set with: GenomicsDBImport Please correct me if I am wrong, but following the tutorials, it seems there are two major options to work with large dataset with Genomic...

• Arye Harel
• October 26, 2020 06:33
• Edited
• 2 followers
• 1 comment
• 0 votes

1. Community
2. General Discussion

a)How do I use GenomicsDBImport for many files and following system criteria Hi, I need to use GenomicsDBImport  on ~250   *.g.vcf.gz  files which sum up together to ~5GB (each file ~10-20MB). I ca...

• Arye Harel
• October 25, 2020 07:26
• Edited
• 2 followers
• 1 comment
• 0 votes

1. Community
2. Germline

How do I obtain vcf file in the BaseRecalibrator  stage of the "Data pre-processing for variant discovery" protocol? Data: Leave plant (non-human) tissue. Hi, I am using GATK to obtain discovery of...

• Arye Harel
• October 19, 2020 12:15
• Edited
• 3 followers
• 8 comments
• 0 votes