Elisabetta Manduchi
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Recent activity by Elisabetta Manduchi Sort by recent activity-
Somatic mutation detection in HLA regions using hg38 alt-aware alignments
AnsweredHello, I'm interested in identifying somatic mutations (using matched samples) both in the non-HLA and HLA regions. For the HLA regions, one approach I've used, was to utilize known HLA-typing inf...
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How to provide custom exon-intron annotation source in Funcotator
Hello, I have used Mutect2 to call somatic variants in the HLA region. Since I had the HLA type for my samples, I aligned the reads for each sample to a reference consisting of the type-specific HL...
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ApplyBQSR for somatic mutation detection in HLA regions
AnsweredHello, I'm a new GATK user and am working on detecting somatic mutations both in non-HLA and HLA regions using Mutect2. For non-HLA mutation calls, I've followed the recommended pipeline both for p...