The Frontline Support team will be offline December 17-18 due to an institute-wide retreat and offline December 22- January 1, while the institute is closed. Thank you for your patience during these next few weeks as we get to all of your questions. Happy Holidays!
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:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
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?