Shahryar Alavi
Genome analysis pipeline developer
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Recent activity by Shahryar Alavi Sort by recent activity-
Because HaplotypeCaller assumes that the input genome is diploid, which is not the case with microbial genomes.
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But MAF output is somewhat different from VCF; and I think the VCF output format is better for germline variant annotation. With Funcotator we get an integrated (and minuter) "variant calling - ann...
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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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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...