Some problems in VCF filtering after GATK HaplotypeCaller step？

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Andrew Zhang

• May 09, 2020 03:40

Can you please provide
a) GATK version used ：4.1.7.0
b) 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 to add DP < min || DP > 2.5 times avrage depth in Hard-filter step? I konw that QualByDepth has already consider the depth value，

（https://gatk.broadinstitute.org/hc/en-us/articles/360035531112--How-to-Filter-variants-either-with-VQSR-or-by-hard-filtering?flash_digest=ac13400bc336bdd6dd909398e8ae385791f336fb#）

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

and  after HaplotypeCaller step, GATK team  don't recommend removing SNPs that are close to indels systematically, while is it necessary to RemoveNearbyIndels

 (https://gatk.broadinstitute.org/hc/en-us/articles/360036430932-RemoveNearbyIndels)

The last one,some papers wrote methods mutation must be supported by at least 2/5 reads each direction,and  I am wondering how to filter this criteria？Use IGV manually to filter？

Look forward to your favourable reply.

 

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  Bhanu Gandham

  • May 10, 2020 23:48

  Hi ,

  The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.

  Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.

  We cannot guarantee a reply, however, we ask other community members to help out if you know the answer.

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