Guruprasad Ananda

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Latest activity by Guruprasad Ananda
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    Guruprasad Ananda created a post,

    IlluminaBasecallsToSam: "INCLUDE_NON_PF_READS" does not appear to work with NovaSeq data


    Hi, IlluminaBasecallsToSam tool provides an option (--INCLUDE_NON_PF_READS) to include non-PF reads in the output demultiplexed BAM files. The default value of this option is "true" and yet we don'...

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    Guruprasad Ananda created a post,

    Incorrect alleles reported by Mutect2

    Hi, we have been using GATK v4.1.4.1 for paired tumor/normal analysis and noticed a discrepancy in the way Mutect2 is calling the REF/ALT alleles at one of the sites.  I've attached an IGV screensh...

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    Guruprasad Ananda commented,

    Hi David Benjamin, I have encountered the same issue that Saba describes in this thread with a couple of low VAF (< 10%) variants, and was wondering if we had any updates on this topic. Thanks.

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    Guruprasad Ananda created a post,

    gnomAD version in Mutect2 bundle

    Hi, which version of gnomAD (2.x.x) and which cohort (exomes or genomes) was used to build the gnomAD VCF file (af-only-gnomad.raw.sites.b37.vcf) that you provide with your mutect2 resource bundle?...