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updated 1 hour ago by
Jorge Amigo
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written 1 day ago by
kmkdesilva
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90
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1 hour ago by
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updated 1 hour ago by
Lluís R.
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written 4 hours ago by
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155
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90 follow
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updated 4 hours ago by
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written 6 hours ago by
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updated 4 hours ago by
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written 3.9 years ago by
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14 hours ago by
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10 hours ago by
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90
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updated 16 hours ago by
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62
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17 hours ago by
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Comment: GATK error: no positional argument is defined for this tool.
by
kamanovae
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Sorry, I tried to fix the error and added an extra input. However, nothing changes even if the last rule looks like this:
rule gatk_Ga…
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You can include any desired combination of conditions using the appropriate [bcftools' expression][1]. In your case, this combination that …
Comment: How to filter a vcf file based on genotype of first two samples
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In fact, you can. I'll post it as a new answer as it really think that should be the way to go.
Comment: Download whole 1000 genome phase 3 for LD clumping
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ahmed.abdo
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Thanks so much, but how download it, I click on the link and nothing appear.
Comment: GATK error: no positional argument is defined for this tool.
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the value of all_samples_BaseRecalibrator is empty. Furthermore, why do you have two `-I` in this command ?
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There's a few options to download the phase 3 VCFs here, including the NCBI FTP site: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp
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Why to do you think that this high power is due to an interesting biological variable and not an uninteresting batch effect? How similar ar…
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Maybe too late but you're on the wrong forum. Ask on [forum.image.sc][1].
[1]: https://forum.image.sc/
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https://www.nature.com/articles/s41588-019-0558-9 , there is a Data Availability statement there, but I doubt it contains the information …
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ANNOVAR is just a suggestion of a software that would read VCF format and translate it into the one you need while retaining the informatio…
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ComplexHeatmap is great, very versatile with lots of options to customize and add features, such as rw and column annotations- and decorati…
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I forgot to inlcude an important piece of information.... I only have access to summary data. Another and much more relevant reason to not …
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No gold standard for this. You can use the closest gene, or the closest expressed genes, or the closest differential gene. That very much d…
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No gold standard for this. You can use the closest gene, or the closest expressed genes, or the closest differential gene. That very much d…
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HI,
PCA will not do the removal thing, it just give you the insight of your data, is it feasible or not?
if in PCA plot, your data separat…
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