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updated 12 weeks ago by
Ram
39k
•
written 8.5 years ago by
f.muoghalu
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25 days ago by
Rafael Soler
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1.2k
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updated 8 months ago by
Matthias Zepper
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written 9 months ago by
A_heath
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updated 6 months ago by
Ram
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written 7.9 years ago by
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updated 5 months ago by
Ram
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written 8.0 years ago by
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2.5k
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6.5k
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10
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3.3k
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updated 10 months ago by
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2.6k
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10
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Ram
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23k
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80
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50
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Recent Replies
Comment: The .vcf format: is there a file format better suited for the era of pangenomics
by
Vincent Laufer
★
3.0k
@ram - this was as bit of a dirty tactic on my part: I stated it in the extreme to provoke disagreement. I agree with you - the irony is, d…
Comment: The .vcf format: is there a file format better suited for the era of pangenomics
by
Ram
39k
> .vcf is the ideal file format for genomic information; no better file format can be conceived whether in the era of singular linear refer…
Comment: GISTIC from ASCAT
by
Ram
39k
You can use pastebin or GitHub gist to paste more lines, maybe you're being restricted because you're a new user. Did GISTIC give you somet…
Comment: Why does Ensembl VEP provide HGVSg for some variants and not others?
by
Jeremy Leipzig
21k
you're right it's an off-by-one-error on my part. thanks
Comment: A question about the raw RNA-seq processing workflow
by
swbarnes2
13k
are files a,b and c all from the same sample? Or are you trying to align three different samples all together?
Comment: multiqc: group samples by population + boxplot ?
by
GenoMax
130k
Tagging: https://www.biostars.org/u/14100/
Rest of this line is required by biostars code.
Comment: Why does Ensembl VEP provide HGVSg for some variants and not others?
by
Vincent Laufer
★
3.0k
@genomax thank you for clarifying that - end of an era!
Comment: Why does Ensembl VEP provide HGVSg for some variants and not others?
by
GenoMax
130k
FYI: Emily no longer works for/at Ensembl. That is the reason she has taken out `_ensembl` from her profile.
https://www.biostars.org/u/23…
Comment: GISTIC from ASCAT
by
Hyper_Odin
▴
280
Sorry, this is how much I could paste, there is an error in the website while pasting more lines
Comment: GISTIC from ASCAT
by
Hyper_Odin
▴
280
Hi Ram, there you go
Sample Chromosome Start Position End Position Seg.CN
metastasis_H021-ARNHGQ0.47_6.segments_final.tx…
Comment: Why does Ensembl VEP provide HGVSg for some variants and not others?
by
Vincent Laufer
★
3.0k
copy that.
also granted your background i expected nothing less :-)
Comment: Why does Ensembl VEP provide HGVSg for some variants and not others?
by
Vincent Laufer
★
3.0k
3 quick questions:
1) are you working with a single sample or multisample VCF?
2) what genomic build? (ill assume GRCh38.p14)
3) do you…
Comment: Why does Ensembl VEP provide HGVSg for some variants and not others?
by
Jeremy Leipzig
21k
yes this should be a reproducible example using just those two lines and the latest vep and database on GRCh38
Comment: GISTIC from ASCAT
by
Ram
39k
Can you show me the first 30 lines from the segmentation file you're passing as input to GISTIC please?
Comment: Why does Ensembl VEP provide HGVSg for some variants and not others?
by
Vincent Laufer
★
3.0k
I have a couple thoughts on this - first, though, would like to confirm that you are on GRCh38?
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