Jeremie Kalfon
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Activity overview
Latest activity by Jeremie Kalfon-
Jeremie Kalfon commented,
of course.. my bad ahah. Thanks again!
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Jeremie Kalfon commented,
This one: https://dockstore.org/workflows/github.com/broadinstitute/gatk/mutect2:4.1.8.1?tab=info
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Jeremie Kalfon commented,
Oh thanks! these are some great ressources.From what I see, I will use M2 with the --genotype-germline-sites set to true in order to maximize variants found and filter found germlines based on AF. ...
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Jeremie Kalfon commented,
Thank you for your answer! "the germline output from Mutect2 are not always as reliable." Is there a good reason as to why, though?
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Jeremie Kalfon commented,
mutect2 also outputs germline mutations in addition to somatic mutations. Why would one go on to use haplotype caller then? What are the advantages / differences?
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Jeremie Kalfon created a post,
haplotypeCaller phasing
AnsweredHi, Does HaplotypeCaller use paired end information (considering paired-ends as a single read), for its phasing? Best,
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Jeremie Kalfon created a post,
Run Germline Tools on Cell Line Genomes
Hello, I am working on the Cancer Cell Line Encyclopedia and I have a question. Assuming a Cell Line is a Cancer genome with perfect purity. What are the advantages of using tools such as mutect,...