Arye Harel
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Recent activity by Arye Harel Sort by recent activity-
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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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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Thank you. In the case of Plant data, and diploid samples. What is the advantage of using Mutect2 over HaplotypeCaller?
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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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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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Hi Anthony,Thank you very much!Sorry for the late response.I am looking in to it now. A.
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Hi Anthony, Thank you very much!Sorry for the late response.I am looking in to it now. A.
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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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Dear Genevieve, Thank you very much for the helpful response. Arik
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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...