GATK-CollectVariantCallingMetrics - regarding more information

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Krithika_Subramanian

• August 04, 2020 14:33

Can you please provide
a) GATK version used : 4.1.2.0
b) Exact GATK commands used :

gatk CollectVariantCallingMetrics \

      INPUT=${input_vcf} \

      OUTPUT=${metrics_basename} \

      DBSNP=${dbSNP_vcf} \

      SEQUENCE_DICTIONARY=${ref_dict} \

      TARGET_INTERVALS=${wgs_evaluation_interval_list} \

      GVCF_INPUT=true

c) The entire error log if applicable. - No error

 

Hi GATK Team,

The above command will generate summary and detailed metrics files. In that there will be Number of common and novel SNPs, InDels and other multiallelic variation. But could you please help me how can I get an information of which position are novel and which position are common when compare to given dbsnps. 

 

Thank you in advance

Krithika S

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  Genevieve Brandt (she/her)

  • August 04, 2020 18:16

  Hi Krithika_Subramanian,

  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.

  For context, check out our support policy.

   

   

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