Marcela Martinez
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Activity overview
Latest activity by Marcela Martinez-
Marcela Martinez created a post,
Not output and not error from GATK CreateSequenceDictionary
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 \ -...
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Marcela Martinez created a post,
Determine Contig Ploidy error_theano.gof.compilelock
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...
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Marcela Martinez created a post,
GATK CNVs Ploidy Interpretation
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...
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Marcela Martinez commented,
Hi, I am planning to run the Germline CNVs in docker on 106 targeted exomes. I am not planning to use the wld pipeline. I already run the Preprocessing step and I wonder how to run the next step, C...
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Marcela Martinez created a post,
MacOs GATK4 Haplotype Caller : AVX instruction set support needed for the accelerated AVX PairHmm
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...
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Marcela Martinez created a post,
Download GATK4 required packages in docker container
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 ...