User: Garan

gravatar for Garan
Garan540
Reputation:
540
Status:
Trusted
Location:
United Kingdom
Website:
https://github.com/pasted
Last seen:
11 hours ago
Joined:
4 years, 7 months ago
Email:
g*********@gmail.com

Posts by Garan

<prev • 36 results • page 1 of 4 • next >
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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 13 days ago by Garan540
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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 6 weeks ago by Garan540
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Answer: A: how to identify disease variants from bam file ?
... Use a variant caller such as GATK HaplotypeCaller, Platypus, SAMtools, FreeBayes, etc. This will give you a VCF (usually) with the Single Nucleotide Variants (SNVs) and InDels (Short insertation / deletion events). If you also want larger variants such as Copy Number Variants (CNVs) and Structural V ...
written 7 weeks ago by Garan540
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Comment: C: CNV analysis from vcf file
... Align the fastq files against the reference genome - BWA or similar against GRCh.v.38 (or 37) - you might want to run the full GATK best practices pipeline. If the sequencing was all done as part of a batch (same flowcells, same library prep) you can run something like ExomeDepth or XHMM (read depth ...
written 11 weeks ago by Garan540
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Comment: C: Most important International Big Data Projects: Genetics and Epigenetics
... I would add [UK Biobank][1] to that list since it's being Exome sequenced and Whole Genome sequenced. I think Tempus RNA stabilisation tubes were collected from participants in addition to samples for DNA sequencing (for phase 2 at least). [1]: http://www.ukbiobank.ac.uk/ ...
written 3 months ago by Garan540
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Answer: A: NA12878 vs RM 8398 Reference DNA
... The NIST source preparation material discusses how RM8398 was extracted from the NA12878 cell. It notes that the cell lines are subject to mutation and so the sequence can start to vary over time. NIST controls for this by producing a large batch of NA12878 and mixing the extracted DNA to reduce the ...
written 3 months ago by Garan540
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Comment: C: Visualizing body organs in R
... Just to add that the github repo has a nice walk through with images of the outputs [https://github.com/jespermaag/gganatogram][1] [1]: https://github.com/jespermaag/gganatogram ...
written 3 months ago by Garan540
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Comment: C: Paternity Testing from WGS Trio
... Or the implementation of the KING algorithm in VCFTools using the -relatedness2 argument [https://vcftools.github.io/man_latest.html][1] [1]: https://vcftools.github.io/man_latest.html ...
written 4 months ago by Garan540
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Comment: C: Down sampling BAM files for CNV detection
... From what the samtools documentation says I think it does keep the mate-pair (just didn't read it first time!) - *"This subsampling acts in the same way on all of the alignment records in the same template or read pair, so it never keeps a read but not its mate"*. For Samtools view -s 42.2, should ...
written 4 months ago by Garan540
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Comment: C: Down sampling BAM files for CNV detection
... Keeping mate-pairs intact - not really an issue for ExomeDepth since it's a coverage based CNV caller, but might be needed if you're comparing to other CNV callers. ...
written 4 months ago by Garan540

Latest awards to Garan

Scholar 3 months ago, created an answer that has been accepted. For A: about the previous version of GATK
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
Supporter 4 months ago, voted at least 25 times.
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Recommendations for CNV calling algorithms/programs to benchmark
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
Scholar 10 months ago, created an answer that has been accepted. For A: about the previous version of GATK
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
Scholar 2.9 years ago, created an answer that has been accepted. For A: about the previous version of GATK
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
Scholar 4.2 years ago, created an answer that has been accepted. For A: about the previous version of GATK
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
Scholar 4.3 years ago, created an answer that has been accepted. For A: about the previous version of GATK

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