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How to extract germline mutations from Mutect2?

princethewinnerprincethewinner Member
edited April 19 in Ask the GATK team
I am interested in performing a study on germline mutations in a cancer patient. VCF files in TCGA reports only somatic mutations. As per the GDC DNA-seq analysis pipeline, they use below command to get somatic mutations-

java -jar GenomeAnalysisTK.jar \
-T MuTect2 \
-R < reference > \
-L < region > \
-I:tumor < tumor.bam > \
-I:normal < normal.bam > \
--normal_panel < pon.vcf > \
--cosmic < cosmic.vcf > \
--dbsnp < dbsnp.vcf > \
--contamination_fraction_to_filter 0.02 \
-o < mutect_variants.vcf > \
--output_mode EMIT_VARIANTS_ONLY \

After reading the MuTect2 documentation, I could not figure out how to modify the above command to retrieve germline mutation from the bam file.


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