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GATK Funcotator and GATK VariantFiltration

Hey there!

I have used GATK Funcotator tool that generated values for plenty of fields as indicated below.

INFO=<ID=FUNCOTATION,Number=A,Type=String,Description="Functional annotation from the Funcotator tool. Funcotation fields are: Gencode_19_hugoSymbol|Gencode_19_ncbiBuild|Gencode_19_chromosome|Gencode_19_start|Gencode_19_end|Gencode_19_variantClassification|Gencode_19_secondaryVariantClassification|Gencode_19_variantType|Gencode_19_refAllele|Gencode_19_tumorSeqAllele1|Gencode_19_tumorSeqAllele2|Gencode_19_genomeChange|Gencode_19_annotationTranscript|Gencode_19_transcriptStrand|Gencode_19_transcriptExon|Gencode_19_transcriptPos|Gencode_19_cDnaChange|Gencode_19_codonChange|Gencode_19_proteinChange|Gencode_19_gcContent|Gencode_19_referenceContext|Gencode_19_otherTranscripts|ClinVar_HGMD_ID|ClinVar_SYM|ClinVar_TYPE|ClinVar_ASSEMBLY|ClinVar_rs|gnomAD_exome_AF|gnomAD_exome_AF_afr|gnomAD_exome_AF_afr_female|gnomAD_exome_AF_afr_male|gnomAD_exome_AF_amr|gnomAD_exome_AF_amr_female|gnomAD_exome_AF_amr_male|gnomAD_exome_AF_asj|gnomAD_exome_AF_asj_female|gnomAD_exome_AF_asj_male|gnomAD_exome_AF_eas|gnomAD_exome_AF_eas_female|gnomAD_exome_AF_eas_jpn|gnomAD_exome_AF_eas_kor|gnomAD_exome_AF_eas_male|gnomAD_exome_AF_eas_oea|gnomAD_exome_AF_female|gnomAD_exome_AF_fin|gnomAD_exome_AF_fin_female|gnomAD_exome_AF_fin_male|gnomAD_exome_AF_male|gnomAD_exome_AF_nfe|gnomAD_exome_AF_nfe_bgr|gnomAD_exome_AF_nfe_est|gnomAD_exome_AF_nfe_female|gnomAD_exome_AF_nfe_male|gnomAD_exome_AF_nfe_nwe|gnomAD_exome_AF_nfe_onf|gnomAD_exome_AF_nfe_seu|gnomAD_exome_AF_nfe_swe|gnomAD_exome_AF_oth|gnomAD_exome_AF_oth_female|gnomAD_exome_AF_oth_male|gnomAD_exome_AF_popmax|gnomAD_exome_AF_raw|gnomAD_exome_AF_sas|gnomAD_exome_AF_sas_female|gnomAD_exome_AF_sas_male|gnomAD_exome_ID|gnomAD_exome_FILTER|gnomAD_genome_AF|gnomAD_genome_AF_afr|gnomAD_genome_AF_afr_female|gnomAD_genome_AF_afr_male|gnomAD_genome_AF_amr|gnomAD_genome_AF_amr_female|gnomAD_genome_AF_amr_male|gnomAD_genome_AF_asj|gnomAD_genome_AF_asj_female|gnomAD_genome_AF_asj_male|gnomAD_genome_AF_eas|gnomAD_genome_AF_eas_female|gnomAD_genome_AF_eas_male|gnomAD_genome_AF_female|gnomAD_genome_AF_fin|gnomAD_genome_AF_fin_female|gnomAD_genome_AF_fin_male|gnomAD_genome_AF_male|gnomAD_genome_AF_nfe|gnomAD_genome_AF_nfe_est|gnomAD_genome_AF_nfe_female|gnomAD_genome_AF_nfe_male|gnomAD_genome_AF_nfe_nwe|gnomAD_genome_AF_nfe_onf|gnomAD_genome_AF_nfe_seu|gnomAD_genome_AF_oth|gnomAD_genome_AF_oth_female|gnomAD_genome_AF_oth_male|gnomAD_genome_AF_popmax|gnomAD_genome_AF_raw|gnomAD_genome_ID|gnomAD_genome_FILTER">

I have used GATK VariantFiltration to apply hard filters with the help of below links.
https://software.broadinstitute.org/gatk/documentation/article.php?id=6925
https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_filters_VariantFiltration.php

However, I would like to know if I would be able to use GATK VariantFiltration tool for applying filters to specific columns of interest obtained from GATK Funcotator say, gnomAD_exome_AF and gnomAD_genome_AF? If yes, could you please let me know how?

Also, is there a way to use GATK Funcotator to report only columns of interest as opposed to all the columns as listed above?

Would appreciate your help.

Amit

Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi ,

    The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal/erroneous 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, see this [announcement](https://software.broadinstitute.org/gatk/blog?id=24419 “announcement”) and check out our [support policy](https://gatkforums.broadinstitute.org/gatk/discussion/24417/what-types-of-questions-will-the-gatk-frontline-team-answer/p1?new=1 “support policy”).

  • amit4biotekamit4biotek Ann ArborMember

    Hi Bhanu,

    Thanks for your reply.

    I learned today that Jonn Smith worked on developing GATK Funcotater. It would be great if he could help me answer my query (of course after holidays!).

    Also, I have one more query to add. I have used GATK Funcotator with Clinvar data source and would like to filter the variants based on clinical significance in Clinvar. However, as you can see from the fields data I provided in my original request, the clinical significance values are not included in annotation despite using the Clinvar data source. Is there a way to include those values? As this will help in filtering out variants that are reported as "Benign" and/or "Likely Benign" in Clinvar.

    Hoping to hear from him on my queries. Would really appreciate his time.

    Amit

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