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How to define the name of the genotype column for MuTect2 VCFs?

szilvaszilva StockholmMember

Hi, as I see, HaplotypeCaller and MuTect1 is reading the name of the sample from the input BAM, in fact from the SM field of the RG line. How can it be assigned in case of MuTect2? All I am getting is a NORMAL and TUMOR column. My command-line is something like:
java -Xmx16g -jar GenomeAnalysisTK.3.7.jar -T MuTect2 -R human_g1k_v37_decoy.fasta -I:normal Normal_70.bam -I:tumor Tumor_71.bam -o test.vcf
and the SM tags in the BAM files are Normal_70 and Tumor_71 respectively.


Best Answer


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