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2. General Discussion

REQUIRED for all errors and issues: a) GATK version used: b) Exact command used: c) Entire program log: ./gatk CreateSequenceDictionary \         -R ${ref}Homo_sapiens_assembly38.fasta \         -...

• Marcela Martinez
• January 07, 2024 14:12
• 2 followers
• 1 comment
• 0 votes

1. Community
2. Germline

Hi, I am running GATK CNVs Germline in the Contig Ploidy step. I have an error related with theano folder. If a delete the folder, then the script goes well but when I tried a new running the error...

• Marcela Martinez
• November 03, 2023 01:07
• 2 followers
• 1 comment
• 0 votes

1. Community
2. Germline

I ran GATK CNVs pipeline for germline detection. Two of 153 human exomes samples show increased (3 rather than 2) ploidy at some chromosomes. I would like to check further which regions of those ch...

• Marcela Martinez
• July 21, 2023 21:04
• 2 followers
• 1 comment
• 0 votes

1. Community
2. Germline

I am running Haplotype Caller of GATK4.0.0, into a docker container in Mac (MacBookPro, Apple M2). I got the following warning message: PairHMM - OpenMP multi-threaded AVX-accelerated native PairHM...

• Marcela Martinez
• April 30, 2023 01:33
• 3 followers
• 2 comments
• 0 votes

1. Community
2. New User Advice

Hello, I have installed GATK4 (version 4.4.0) in a docker container in MacOS following the published instructions (https://gatk.broadinstitute.org/hc/en-us/articles/360035889991). I also created a ...

• Marcela Martinez
• April 25, 2023 22:29
• 2 followers
• 1 comment
• 0 votes