User: Garan

gravatar for Garan
Garan650
Reputation:
650
Status:
Trusted
Location:
United Kingdom
Website:
https://github.com/pasted
Last seen:
1 week ago
Joined:
6 years, 6 months ago
Email:
g*********@gmail.com

Posts by Garan

<prev • 49 results • page 1 of 5 • next >
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Answer: A: ICD10, main ICD10 and secondary ICD10
... I think it's the main HES data that you want with 410,309 participants, which I believe is **41270** Diagnoses - ICD10 (this should be a combination of both main diagnoses 41202 and any secondary diagnoses 41204). You can see how the data is derived for 41270 in the Related Data-fields tab for 4127 ...
written 4 weeks ago by Garan650
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Answer: A: Best way for CNV phenotype association analysis.
... I think if it's a case-control model then it would be a logistic regression? In this paper on arthrometric traits they use linear regression on CNVs (these would be mainly germline CNVs predicted from microarray data) and linear anthropometric traits such as height and weight in the UK Biobank data ...
written 9 months ago by Garan650
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Answer: A: ExomeDepth failure to run
... You could try installing from vplagnol github repository (using DevTools) to see if the dependency has been updated (GRanges) [https://github.com/vplagnol/ExomeDepth][1] install.packages("devtools") library(devtools) install_github("vplagnol/ExomeDepth") If it hasn't then you cou ...
written 12 months ago by Garan650
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Comment: C: tools for MLST analysis
... Any particular bacterial species? Public Health England has one for Salmonella, although it's abit old now: [https://github.com/phe-bioinformatics/MOST][1] [1]: https://github.com/phe-bioinformatics/MOST ...
written 12 months ago by Garan650
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Comment: C: Associate SNPs with Clinical Data
... Couldn't you use a large population study such as UK Biobank as your controls? There is some WES data (50K or so participants at this time, although all 500K should be done eventually), although you could just convert the variant calls from from the WES data to the SNP alleles that match the UK Biob ...
written 14 months ago by Garan650
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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 16 months ago by Garan650
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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 17 months ago by Garan650
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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 18 months ago by Garan650
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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 19 months ago by Garan650
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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 19 months ago by Garan650

Latest awards to Garan

Scholar 12 months ago, created an answer that has been accepted. For A: about the previous version of GATK
Scholar 2.2 years ago, created an answer that has been accepted. For A: about the previous version of GATK
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
Supporter 2.2 years ago, voted at least 25 times.
Good Answer 2.3 years ago, created an answer that was upvoted at least 5 times. For A: Recommendations for CNV calling algorithms/programs to benchmark
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
Scholar 2.8 years ago, created an answer that has been accepted. For A: about the previous version of GATK
Teacher 2.8 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
Teacher 5.6 years ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
Teacher 6.0 years ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
Scholar 6.0 years ago, created an answer that has been accepted. For A: about the previous version of GATK
Teacher 6.0 years ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
Scholar 6.2 years ago, created an answer that has been accepted. For A: about the previous version of GATK

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