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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

FilterMutectCalls Problems

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    Gökalp Çelik

    Hi lei yang

    Does Mutect2 produce a proper VCF output? Do you observe calls in that file?

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    lei yang

    Thanks for your reply, I think Mutect2 produces a proper vcf . File size is 4M

    ##tumor_sample=S1135
    #CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO
    chr1    14932    .    G    T    .    .    AS_SB_TABLE=0,0|0,0;DP=2;ECNT=2;MBQ=40,33;MFRL=393,306;MMQ=22,22;MPOS=36;POPAF=2.00;TLOD=3.72
    chr1    14937    .    T    C    .    .    AS_SB_TABLE=0,0|0,0;DP=2;ECNT=2;MBQ=35,28;MFRL=393,306;MMQ=22,22;MPOS=31;POPAF=2.11;TLOD=3.72
    chr1    19004    .    A    G    .    .    AS_SB_TABLE=3,0|2,0;DP=5;ECNT=1;MBQ=33,28;MFRL=353,348;MMQ=22,21;MPOS=19;POPAF=0.357;TLOD=3.27
    chr1    135465    .    C    T    .    .    AS_SB_TABLE=0,2|0,2;DP=4;ECNT=1;MBQ=28,33;MFRL=379,325;MMQ=40,40;MPOS=19;POPAF=0.650;TLOD=6.08

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    Gökalp Çelik

    Hi lei yang

    Are these the whole variant contexts from the VCF? Are you using the parameter below?

    --sites-only-vcf-output

    These variant contexts do not have any genotype information therefore it is probably normal that FilterMutectCalls is not working. 

    Let us know what your Mutect2 parameters are and if you are performing any other post processing before FilterMutectCalls step. 

    Regards. 

     

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