Shahryar Alavi

Genome analysis pipeline developer

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Latest activity by Shahryar Alavi
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    Shahryar Alavi created a post,

    Split and trim multiallelic sites, whitout missing genotype info

    I have a cohort of 200 whole-exomes for which I've created a table of variants with their frequencies. I want to analyse new exomes and filter their frequent variants based on my cohort. But the mu...

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    Shahryar Alavi commented,

    The increment argument efficiently speeds up DB renewal: gatk GenomicsDBImport --genomicsdb-update-workspace-path path/to/DB --sample-name-map new_samples.map --batch-size 45 But, is it possible to...

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    Shahryar Alavi commented,

    What about duplicated genes? To my knowledge, GATK does not call variants if reads are mapped to more than one locus on the genome; e.g. we never see variants of SMN1 and SMN2 genes in our annotate...