Arye Harel
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Activity overview
Latest activity by Arye Harel-
Arye Harel created a post,
Is "Somatic short variant discovery" the correct Pipeline to identify differential microsatellites?
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...
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Arye Harel commented,
Please let me know if you have answer to my question. Thank you.
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Arye Harel created a post,
How to identify differential microsatellites in GATK ?
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...
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Arye Harel commented,
Regarding the first Usage examples on top on of this page: What does -L 20 mean? If used, it gives the following Error: "A USER ERROR has occurred: Badly formed genome unclippedLoc: Query interval ...
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Arye Harel created a post,
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...
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Arye Harel created a post,
Recommended parameters for GenomicsDBImport
Answereda)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...
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Arye Harel commented,
Dear Genevieve, Thank you very much for the helpful response. Arik
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Arye Harel commented,
One more question: Looking at "https://gatk.broadinstitute.org/hc/en-us/articles/360035535912-Data-pre-processing-for-variant-discovery", it reads: "Tools involved: BaseRecalibrator, Apply Recalibr...
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Arye Harel commented,
Hi Genevieve, Thank you for your fast response.I am missing a vcf file.These are the main stages and files I already ran: 1. Task: QASoftware: fastqcInput: individualA_f.fq.gz , individualA_r.fq...
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Arye Harel created a post,
Data pre-processing for variant discovery - BaseRecalibrator, vcf input?
AnsweredHow 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...