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Duplicate mutation in oncotator output

The following steps are used in mutation calling with matched normal:
1. MuTect if used for mutation call, generating VCF output. The command line is:
java -Xmx8g -jar XXXX.jar -T MuTect -R GRCh37.fa --dbsnp dbsnp_138.b37.vcf --cosmic b37_CosmicCodingMuts_v70.vcf --cosmic b37_CosmicNonCodingVariants_v70.vcf --tumor_sample_name TUMOR --input_file:tumor tumor.bam --out call_stats.txt --coverage_file coverage.wig.txt --vcf mutect.out.vcf --normal_sample_name NORMAL --input_file:normal normal.bam

A couple of data line in the VCF is here:
1 10231 rs200279319 C A . REJECT DB GT:AD:BQ:DP:FA 0:2,0:.:1:0.00 0/1:0,1:33:1:1.00
1 10419 . T G . REJECT . GT:AD:BQ:DP:FA 0:11,3:.:8:0.214 0/1:3,0:.:3:0.00
1 10425 . T G . REJECT . GT:AD:BQ:DP:FA 0:7,5:.:8:0.417 0/1:2,0:.:2:0.00

2. Oncotator is used for annotate the vcf file generated by MuTect. THe command line is:

oncotator --input_format=VCF --db-dir oncotator_v1_ds_Jan262015 -c tx_exact_uniprot_matches.AKT1_CRLF2_FGFR1.txt mutect.out.vcf oncotator.maf.txt hg19

A couple of data line in the VCF is here: (I only show first couple of columns):
Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_position End_position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 Tumor_Sample_Barcode Matched_Norm_Sample_Barcode
DDX11L1 100287102 __UNKNOWN__ __UNKNOWN__ 1 10231 10231 __UNKNOWN__ RNA SNP C C A rs200462216|rs200279319|rs376846324 __UNKNOWN__ NORMAL
DDX11L1 100287102 __UNKNOWN__ __UNKNOWN__ 1 10231 10231 __UNKNOWN__ RNA SNP C C A rs200462216|rs200279319|rs376846324 __UNKNOWN__ TUMOR

For each mutation in the VCF from MuTect, ex, chr1 10231, it has two records in the Oncotator output: one record with the filed "Matched_Norm_Sample_Barcode" = NORMAL, the other record with the field "Matched_Norm_Sample_Barcode" = TUMOR. Also, for both records, the field "Tumor_Sample_Barcode" is set to be "__UNKNOWN__".

1. What does this mean? Can I have the correct content for "Tumor_Sample_Barcode" and "Matched_Norm_Sample_Barcode"?
2. For the file above generated by Oncotor, I only need the Somatic mutation in tumor sample comparing to the normal sample. Unfortunately, the one with "Matched_Norm_Sample_Barcode" = TUMOR is the right one, with t_alt_count equals to the number of reads covering this mutation base in the tumor sample. It's very confusing. How to make it right?



  • pachomppachomp OregonMember

    Hi Jeremy,

    I can throw out a couple of possibilities for you, though the definitive answer should come from someone on the GATK team.

    For your first question, I would guess that you don't have your barcode read group (platform unit?) set, and therefore Oncotator has nothing to put in that column.

    For your second question, if you want to only include the tumor sample in your Oncotator output, you would need to manipulate the input VCF. If I wanted to do this, I would use GATK's SelectVariants, and tell it to only grab the tumor sample. I can say though, it is sometimes nice to compare read counts between the tumor and normal directly from Oncotator, but that would be a use-specific decision.


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Both answers are correct. We can't provide you with barcode information, that's a property of your own data.

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