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whynot

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  • Mutect2 : annotation group & fields that can check strand bias

    1. Community
    2. Somatic

    Hi :) I want to check the strand bias in the vcf file.   So I check default annotation (group). > Mutect2 : Default annotation group = [StandardMutectAnnotation] > HaplotypeCaller : Default annotat...

    • whynot
    • 2 followers
    • 1 comment
    • 0 votes

  • What is the 'physical phasing'

    1. Community
    2. Other

    Hi I wonder about PGT of VCF format field.   According to the meta-information line, ##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the al...

    • whynot
    • 4 followers
    • 3 comments
    • 0 votes

  • Mutect2 filter : clustered_events definition

    Answered
    1. Community
    2. Somatic

    Hi. I'm student who study bioinformatics. I make some vcf files using GATK3.6 tumor only mode.   I wonder about 'clustered_events' filter's definition. According to the vcf meta-information line,  ...

    • whynot
    • 4 followers
    • 7 comments
    • 0 votes