User: Garan

gravatar for Garan
Garan530
Reputation:
530
Status:
Trusted
Location:
United Kingdom
Website:
https://github.com/pasted
Last seen:
an hour ago
Joined:
4 years, 3 months ago
Email:
g*********@gmail.com

Posts by Garan

<prev • 32 results • page 1 of 4 • next >
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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 days ago by Garan530
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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 days ago by Garan530
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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 5 days ago by Garan530
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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 9 days ago by Garan530
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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 weeks ago by Garan530
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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 weeks ago by Garan530
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Comment: C: Down sampling BAM files for CNV detection
... **-s FLOAT** Output only a proportion of the input alignments. 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. The integer and fractional parts of the -s INT.FRAC option are used separately ...
written 4 weeks ago by Garan530
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Answer: A: HLA Typing understanding
... I think the readme on the download site might have the answer: The HLA typing data of 1,267 individuals related to the 1000 Genomes Project (Table 1) covers 14 populations encompassing 4 major ancestral groups. After specific PCR amplification, exons were sequenced by Sanger technique. The sequen ...
written 4 weeks ago by Garan530
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Answer: A: How to select an aligner?
... Might also want to look at Minimap2 by Heng Li [https://github.com/lh3/minimap2][1] [https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/bty191/4994778][2] Has a nice introductory tutorial and the readme gives some great examples. *Minimap2 is a versatile ...
written 3 months ago by Garan530
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Answer: A: Recommendations for CNV calling algorithms/programs to benchmark
... I'm guessing you're after germline CNV callers since you've mentioned CNVnator. I've included some suggestions below for read-depth based callers including ExomeDepth which is the one I've used the most (reasonably easy to use since it's an R package). I'd have a look at Ximmer if you're interested ...
written 7 months ago by Garan530

Latest awards to Garan

Scholar 3 days ago, created an answer that has been accepted. For A: about the previous version of GATK
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
Supporter 9 days ago, voted at least 25 times.
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: Recommendations for CNV calling algorithms/programs to benchmark
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
Scholar 7 months ago, created an answer that has been accepted. For A: about the previous version of GATK
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
Scholar 2.6 years ago, created an answer that has been accepted. For A: about the previous version of GATK
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
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 3.8 years ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
Scholar 3.8 years ago, created an answer that has been accepted. For A: about the previous version of GATK
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
Scholar 4.0 years ago, created an answer that has been accepted. For A: about the previous version of GATK

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