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whynot

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Latest activity by whynot
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    whynot created a post,

    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
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    whynot created a post,

    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
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    whynot commented,

    1. Community
    2. Somatic
    3. Mutect2 filter : clustered_events definition

    Thanks for answer!   Can I have one more question?   I got new information about clustered_events filter. When they count 'clustered' variants, they have another condition: "variants with distance ...

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    whynot created a post,

    Mutect2 filter : clustered_events definition

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    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
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