User: Garan

gravatar for Garan
Garan570
Reputation:
570
Status:
Trusted
Location:
United Kingdom
Website:
https://github.com/pasted
Last seen:
2 hours ago
Joined:
5 years, 1 month ago
Email:
g*********@gmail.com

Posts by Garan

<prev • 44 results • page 1 of 5 • next >
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Comment: C: how to perform GWAS on UKBiobank data?
... You might want to try BOLT-LMM [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6309610/][1], it's what we currently use for our analysis of UK Biobank data. We're also looking at using SAIGE but don't have the run times for UK Biobank yet. [1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6309610/ ...
written 6 days ago by Garan570
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Comment: C: structural variants in gnomad and the VCF spec. Why is tabix/bcftools failing ?
... Isn't SVTYPE=CTX a hold-over from TIGRA-SV? Maybe it's due to support in GRanges readVCF for non-compliant VCF SV types? Not that this would help with BCFTools but it might be an explanation as to how these SV annotations made it into Gnomad. https://bioconductor.org/packages/devel/bioc/vignettes/S ...
written 23 days ago by Garan570
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Answer: A: Gold standard CNV Calls for NA12878
... Have you tried some of the Genome In A Bottle resources? [https://jimb.stanford.edu/giab-resources][1] **EDIT** Recent paper by the GIAB group https://www.biorxiv.org/content/10.1101/664623v1 Mt. Sinai School of Medicine has uploaded ~44x PacBio data for NA12878, including raw reads, error-correc ...
written 9 weeks ago by Garan570
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Comment: C: How can I do in GTAK downstream analysis?
... I guess if you're looking for somatic mutations not germline variants then this complicates things, without non-tumor samples to compare to. I guess you'd also want to take into account the source and age profile of the Gnomad/Exac variant information since I believe some of datasets were recruited ...
written 12 weeks ago by Garan570
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Answer: A: How can I do in GTAK downstream analysis?
... I take it this is a mendelian rare disease that you are looking for a causal variant? Are the 20 samples trios (parents-proband) or singletons (unrelated cases with similar symptoms), as this will change the filtering strategy? Do you have family history? Population details / Phenotype details? If ...
written 12 weeks ago by Garan570
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Answer: A: gnomAD: query utilitites
... The Cellbase Swagger restful API might have what you're after, although I'm not sure how many requests it will take if you're looking to bulk query. [http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/][1] [http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/rest/v4/hsapiens/feature/variation/rs11658 ...
written 3 months ago by Garan570
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Comment: C: Storing Varaint data from VCF
... Just to add to the edit I made to the answer: The processing of the VCFs doesn't have to be straight away, you could set up a scheduler to process the files later, and probably just as important to re-annotate the variants on an ongoing basis (keeping the original version). ...
written 4 months ago by Garan570
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Answer: A: Storing Varaint data from VCF
... I developed something similar a long time ago and you're welcome to have a look [https://github.com/pasted/clinical_variant_database][1] It can probably be improved alot. Things to note: - Variants can be of any size so you probably need a start / stop field for the genomic coordinates - The coo ...
written 4 months ago by Garan570
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Answer: A: Anyone know of a useful pedigree drawing program?
... You could try OmicsTools website for some ideas (many are commercial though) [https://omictools.com/pedigree-drawing-category][1], or the University of Alabama at Birmingham's site [https://www.soph.uab.edu/ssg/linkage/pedigreedrawing][2] For suggestions from previously used software i'd go with s ...
written 6 months ago by Garan570
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Answer: A: Germline CNV Databases for Healthy and/or Cancer Patients
... You could try the Genome In A Bottle reference SV calls v0.6. They are for the HG002 (NA24385 PGP Ashkenazim Jewish Son) genome so shouldn't contain any rare pathogenic CNVs/SVs, but should have common SVs across the genome ("Healthy " germline copy number variation). [ftp://ftp-trace.ncbi.nlm.nih ...
written 7 months ago by Garan570

Latest awards to Garan

Scholar 10 months ago, created an answer that has been accepted. For A: about the previous version of GATK
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
Supporter 10 months ago, voted at least 25 times.
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Recommendations for CNV calling algorithms/programs to benchmark
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
Scholar 16 months ago, created an answer that has been accepted. For A: about the previous version of GATK
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
Scholar 3.4 years ago, created an answer that has been accepted. For A: about the previous version of GATK
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
Scholar 4.7 years ago, created an answer that has been accepted. For A: about the previous version of GATK
Teacher 4.7 years ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
Scholar 4.8 years ago, created an answer that has been accepted. For A: about the previous version of GATK

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