Moderator: dariober
dariober ♦ 9.3k
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Posts by dariober
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... Hi- If it's genotyping arrays you are referring to, then you could try [ASCAT][1]. ASCAT is designed to detect copy number variants and it gives, in addition, the purity estimate.
[1]: https://www.crick.ac.uk/research/labs/peter-van-loo/software ...
written 3 days ago by
dariober ♦ 9.3k
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... Hi- See if this blog post helps you http://varianceexplained.org/statistics/interpreting-pvalue-histogram/ . To get better answers, it would be good to give some background about what you are testing as the U-shape may or may not be anything to worry about. ...
written 11 days ago by
dariober ♦ 9.3k
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Comment:
C: Download of dbSNP VCF file
... To add to yours and Agata's answers (+1), indels can be extracted with `bcftools view -v indels mysnps.vcf.gz`, see [bcftools][1]. (I would resist the temptation of parsing vcf as text using per/python/awk scripts.)
[1]: https://samtools.github.io/bcftools/bcftools.html ...
written 22 days ago by
dariober ♦ 9.3k
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... See if this script, [localEnrichmentBed.py][1], is of any help. See also https://www.biostars.org/p/195689/
[1]: https://github.com/dariober/bioinformatics-cafe/tree/master/localEnrichmentBed ...
written 25 days ago by
dariober ♦ 9.3k
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Answer:
A: ngs vs microarray
... I don't have much experience with genotyping arrays but I think these are an example where arrays are still superior to NGS. If you want to profile a sample at known SNPs genomewide, then it's going to be difficult for NGS to beat arrays in terms of cost, amount of data to process and accuracy. I th ...
written 4 weeks ago by
dariober ♦ 9.3k
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... I haven't thought carefully about your question but the first explanation that comes to my mind is that proportional Venn diagrams with 3 or more sets are not always possible. See this post https://www.biostars.org/p/77362/. ...
written 5 weeks ago by
dariober ♦ 9.3k
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... Well spotted! Corrected now. ...
written 5 weeks ago by
dariober ♦ 9.3k
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... Just as a warning, strictly speaking, it is not possible to extract reads supporting a variant in a VCF since you don't know what reads the underlying variant caller has used. Mutect2, for example, discard reads failing some configurable options about base quality, mapping quality, flags etc plus re ...
written 8 weeks ago by
dariober ♦ 9.3k
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... This would be a nice tool indeed. For visualization, the program I've written, [ASCIIGenome](http://asciigenome.readthedocs.io/en/latest/index.html), has the option [filterVariantReads](http://asciigenome.readthedocs.io/en/latest/commandHelp.html#filtervariantreads) that gets close to what you need ...
written 8 weeks ago by
dariober ♦ 9.3k
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... I was going to suggest CalculateContamination. For more detail about the method see also section VI of [mutect.pdf](https://github.com/broadinstitute/gatk/blob/master/docs/mutect/mutect.pdf). ...
written 8 weeks ago by
dariober ♦ 9.3k
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