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3. RemoveNearbyIndels: CRSP

Hi Bhanu, It is to use the candidate list currently obtained through the VCF file of the parents and child. Then through some reasonable steps, reduce the false positive rate of spontaneous mutatio...

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• Andrew Zhang
• May 18, 2020 01:17
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1. Community
2. Other
3. RemoveNearbyIndels: CRSP

Hello Bhanu： Many thanks，I am wondering is it necessary to remove nearby INDEL，when I was trying to get the de novo  mutation using HaplotypeCaller.

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• Andrew Zhang
• May 17, 2020 07:21
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1. Tool Index
2. 4.0.9.0
3. RemoveNearbyIndels

This is a preprocessing step for the CRSP sensitivity validation truth data" what's the meaning of "CRSP", Clinical Research Sequencing Platform (CRSP)?

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• Andrew Zhang
• May 13, 2020 06:56
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1. Community
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3. RemoveNearbyIndels: CRSP

Not  a googlable question....  

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• Andrew Zhang
• May 13, 2020 06:49
• 0 votes

1. Getting Started
2. Tutorials
3. (How to) Filter variants either with VQSR or by hard-filtering

Very useful ! Well, I am wondering if the data is whole genome sequencing，is it necessary to add DP < min || DP > 2.5 times avrage depth in Hard-filter step?  Look forward to your favourable reply.  

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• Andrew Zhang
• May 08, 2020 02:28
• 1 vote