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PostsRecent activity by Arye Harel Sort by recent activity
In case there is no vcf file from genome project, is it still possible to use the GetPileupSummaries?
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...
Is "Somatic short variant discovery" the correct Pipeline to identify differential microsatellites?Answered
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...
How to identify differential microsatellites in GATK ?Answered
REQUIRED for all errors and issues: a) GATK version used: gatk4-v18.104.22.168 (Can use also gatk3-v3.8.0)b) Exact command used: NAc) Entire program log: NA Hi, Which protocol should be used for microsat...
How to work with large data set with: GenomicsDBImport
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...
Recommended parameters for GenomicsDBImportAnswered
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...
Data pre-processing for variant discovery - BaseRecalibrator, vcf input?Answered
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...