No t_depth in Funcotator MAF

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sahuno

• March 30, 2021 13:43

Is there a way to enable t_depth in Funcotator MAF ? 

however my final maf contains some info on depth  "tumor_f","t_alt_count","t_ref_count","n_alt_count","n_ref_count" 

Thanks in advance

-S

 

GATK version; v4.1.8.1

GATK commands used 

gatk --java-options "-Xmx15500m" Funcotator \
--data-sources-path $DATA_SOURCES_FOLDER \
--ref-version hg38 \
--output-file-format MAF \
-R gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta \
-V gs://fc-1f2cec15-4c83-4842-8fde-c79a1131b2dd/765245fe-26bc-4baf-a969-1e7a2b951215/Mutect2/f8e12ad1-40f7-4a63-82bc-bfe77754cb5e/call-FilterAlignmentArtifacts/CC10010_Tumor.hg38-filtered.vcf \
-O CC10010_Tumor.hg38-filtered.annotated.maf \
-L /cromwell_root/fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/Exome-Agilent_V6_UTR.bedTo.list.interval_list \
--annotation-default normal_barcode:SC173897 \
--annotation-default tumor_barcode:SC173855 \
--annotation-default Center:Unknown \
--annotation-default source:CRC_PR \
--transcript-list /cromwell_root/broad-public-datasets/funcotator/transcriptList.exact_uniprot_matches.AKT1_CRLF2_FGFR1.txt --remove-filtered-variants

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• 

  Genevieve Brandt (she/her)

  • March 30, 2021 17:11

  Hi sahuno,

  I am going to move your post into our Community Discussions -> General Discussion topic, as the Somatic topic is for reporting bugs and issues with GATK.

  You can read more about our forum guidelines and the topics here: Forum Guidelines.

  Best,

  Genevieve

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  Genevieve Brandt (she/her)

  • May 04, 2021 17:55
  • Edited

  Hi sahuno,

  There is no t_depth in the Funcotator MAF. We use the TCGA 2.4.1 MAF spec, which does not include t_depth. We did notice that t_depth is in the GDC MAF 1.0, but the one we use is different. 

  You can calculate the t_depth by adding the t_alt_count and the t_ref_count.

  Best,

  Genevieve

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