
Degang Wu
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Activity overview
Latest activity by Degang Wu-
Degang Wu commented,
@Saeed GATK will leave the commands used to call the genotypes in the header, so you can infer from there whether your vcfs we're joint-called or not.
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Degang Wu commented,
Hi Genevieve Brandt, I read the document in that link before, and I have just gone through it again in case I missed updates to the document. The document does not address my question. The document...
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Degang Wu commented,
If guideline on sensitivity threshold for indel VQSR model is not available, how about a threshold on VQS LOD? Any suggestions are welcome.
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Degang Wu created a post,
How do I choose the "optimal" VQSR sensitivity threshold for indels?
For SNPs, we can choose the inflection point in the novel TiTv vs. sensitivity graph, but I have no idea what principle I should use when choosing the sensitivity threshold for indel.
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Degang Wu created a post,
Best practice to deal with spanning deletion for downstream analysis
AnsweredHello everyone! I'm referring to this article on spanning deletion. Representing spanning deletion with * is good in itself, but unfortunately most of the downstream analysis tools I know cannot de...
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Degang Wu commented,
Representing spanning deletion by * is good in itself, but most of the downstream bioinformatics software I know cannot take care of spanning deletion. Therefore, is there a tool to convert * into ...
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Degang Wu commented,
Nice article. In addition to the dead link reported by Micahel, I would also like to report that the link to "PL and GQ" is also dead.
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Degang Wu commented,
Hello, Could anyone explain the meaning of "rescueing genotype calls" under section titled "2. Greater sensitivity for low-frequency variants"? Does it mean the genotype calls of the low-frequency ...