1. Community
2. Germline
3. How do I choose the "optimal" VQSR sensitivity threshold for indels?

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
• February 11, 2021 01:51
• 0 votes

1. Community
2. Germline
3. How do I choose the "optimal" VQSR sensitivity threshold for indels?

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
• February 10, 2021 14:34
• Edited
• 0 votes

1. Technical Documentation
2. Glossary
3. Spanning or overlapping deletions (* allele)

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
• November 05, 2020 02:53
• 2 votes

1. Technical Documentation
2. Algorithms
3. Assigning per-sample genotypes (HaplotypeCaller)

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
• September 17, 2020 02:16
• 2 votes

1. Technical Documentation
2. Algorithms
3. The logic of joint calling for germline short variants

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 ...

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• Degang Wu
• April 13, 2020 05:47
• 0 votes