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MuTect is Picking up Germline Mutations that are in dbSNP

Haiying7Haiying7 Heidelberg, GermanyMember

I ran MuTect to identify somatic mutations from paired samples of normal (blood) and tumor.
Some of the somatic mutations that the software identified are in dbSNP as germline mutations.
The command line for running MuTect is:

/usr/bin/java -Xmx4g -jar ${MuTect}mutect-1.1.7.jar     \
--input_file:normal ${BQSR_dir}${Blood}.recal.bam --input_file:tumor ${BQSR_dir}${Tumor}.recal.bam    \
--out ${MuTect_dir}${Blood}_${Tumor}_call_stats.out     \
--coverage_file ${MuTect_dir}${Blood}_${Tumor}_coverage.wig.txt    \
--vcf ${MuTect_dir}${Blood}_${Tumor}.vcf  \
--analysis_type MuTect --reference_sequence ${GATK_hg} --cosmic ${COSMIC} --dbsnp ${dbSNP} --intervals ${Intervals}    \

Could someone please take a look and see if I am missing any thing?

Thanks in advance.



  • Haiying7Haiying7 Heidelberg, GermanyMember

    The dbSNP database I am using is downloaded from GATK reference data bundle.
    Would it be possible that the somatic mutations that MuTect identified and that also appearing on dbSNP are just added to dbSNP recently, later than the datbase in GATK bundle?

  • SheilaSheila Broad InstituteMember, Broadie, Moderator


    Can you try using MuTect2 and see if those dbSNP mutations are still picked up?


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