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Andrew Zhang

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  • Total activity 17
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Latest activity by Andrew Zhang
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    Andrew Zhang commented,

    1. Community
    2. Other
    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 commented,

    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 commented,

    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 commented,

    1. Community
    2. Other
    3. RemoveNearbyIndels: CRSP

    Not  a googlable question....  

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    Andrew Zhang created a post,

    RemoveNearbyIndels: CRSP

    1. Community
    2. Other

      "This is a preprocessing step for the CRSP sensitivity validation truth data" what's the meaning of "CRSP", Clinical Research Sequencing Platform (CRSP)? https://gatk.broadinstitute.org/hc/en-us/...

    • Andrew Zhang
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    Andrew Zhang created a post,

    Some problems in VCF filtering after GATK HaplotypeCaller step？

    1. Community
    2. General Discussion

    Can you please provide a) GATK version used ：4.1.7.0b) Exact GATK commands used c) The entire error log if applicable. First， I am wondering if the data is whole genome sequencing，is it necessary t...

    • Andrew Zhang
    • 2 followers
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    Andrew Zhang commented,

    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.