Arye Harel
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Activity overview
Latest activity by Arye Harel-
Arye Harel commented,
Thank you. How would you recommend to generate a set of "known variant" by bootstrap? Which protocol would you recommend? A.
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Arye Harel commented,
Hi Anthony, Thank you very much. >You'll need to run the tool with multiple samples (between 20-50). Will it work well for smaller experiment of 12 samples? >Set your allele frequency cut off ne...
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Arye Harel commented,
Thank you. In the case of Plant data, and diploid samples. What is the advantage of using Mutect2 over HaplotypeCaller?
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Arye Harel commented,
Dear Anthony The entire log is very long, I present the important details. More important- I am not sure it makes sense to use vcf resulting from Mutect2. Thus the important questions are:* Is ther...
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Arye Harel created a post,
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...
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Arye Harel commented,
Hi, I see you sent an improved answer on my duplicated post at: https://gatk.broadinstitute.org/hc/en-us/community/posts/6809415185947-Is-Somatic-short-variant-discovery-the-correct-Pipeline-to-ide...
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Arye Harel commented,
Hi Anthony,Thank you very much!Sorry for the late response.I am looking in to it now. A.
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Arye Harel commented,
Hi Anthony, Thank you very much!Sorry for the late response.I am looking in to it now. A.
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Arye Harel created a post,
Is "Somatic short variant discovery" the correct Pipeline to identify differential microsatellites?
AnsweredRegarding 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 created a post,
How to identify differential microsatellites in GATK ?
AnsweredREQUIRED 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...