Elisabetta Manduchi
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Activity overview
Latest activity by Elisabetta Manduchi-
Elisabetta Manduchi commented,
I think you may be able to get it from Docker, maybe here https://hub.docker.com/layers/sachet/polysolver/v4/images/sha256-4ca4f341da48058c32061137371dd3adb4ea816750a4adfa2a7cc40b730ac6af
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Elisabetta Manduchi commented,
Thank you David Benjamin. Indeed my first approach was along the lines of Polysolver. I've also tried to use the Polysolver docker itself as is, which however did not yield any results in my case.
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Elisabetta Manduchi created a post,
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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Elisabetta Manduchi commented,
Great, thanks for the clarification! Elisabetta
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Elisabetta Manduchi commented,
Thanks for responding Genevieve! The tutorial you indicate coincides with the one I was mentioning in my message, where I found that snippet whose screenshot I sent. Reading the user-defined data s...
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Elisabetta Manduchi created a post,
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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Elisabetta Manduchi commented,
Thanks Genevieve, I really appreciate your feedback. Regarding the build, just to clarify, I'm only aligning to b37 for the non-HLA analyses. For HLA I'm aligning to the type-specifc allele sequenc...
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Elisabetta Manduchi commented,
Thank you so much for your response Genevieve, which confirms my initial intuition. If I may tap into your experience with this type of analysis, I do have a couple of related questions. First, I ...
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Elisabetta Manduchi commented,
Thank you Pamela and sorry for originally posting under the incorrect topic. Elisabetta
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Elisabetta Manduchi created a post,
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...