User: Aliaksei Holik

gravatar for Aliaksei Holik
Reputation:
170
Status:
New User
Location:
Spain, Barcelona, CRG
Twitter:
@AliakseiHolik
Scholar ID:
Google Scholar Page
Last seen:
2 years, 2 months ago
Joined:
3 years, 7 months ago
Email:
s*******@bio.bsu.by

I'm a post-doctoral researcher working in cancer bioinformatics. My main project is looking at the role of regulatory variants in cancer predisposition. But I also look at a lot of RNA-seq, ChIP-seq, chromatin accessibility and chromatin conformation data.

Posts by Aliaksei Holik

<prev • 4 results • page 1 of 1 • next >
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Comment: C: Remove positions that are non-variant in a subset of samples from a vcf file
... Thank you Chris. I'll give it a try, once I get GATK to run. ...
written 2.3 years ago by Aliaksei Holik170
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Comment: C: Remove positions that are non-variant in a subset of samples from a vcf file
... Thanks! I had the suggestion for GATK SelectVariants from somebody else as well, but wasn't able to get past making it to run :( So still not tested, but it looks promising. ...
written 2.3 years ago by Aliaksei Holik170
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Answer: A: Remove positions that are non-variant in a subset of samples from a vcf file
... After much searching and discussions with colleagues there are several solutions that seem to work here. ## Solution one - pure **bcftools**: ## This is a bit of an indirect solution, as it relies on the AC (allele count) field to "guess" if there are ANY genotypes other than 0/0 for a given varia ...
written 2.3 years ago by Aliaksei Holik170
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Remove positions that are non-variant in a subset of samples from a vcf file
... Hi all, I have a multi-sample vcf file and I would like to produce a new vcf file containing a subset of samples, while excluding the variants that don't have any alternative allele genotypes in that subset of samples (i.e. exclude all the variants with genotype 0/0). I can use vcf tools to extract ...
vcf bcftools vcftools genotype filtering written 2.3 years ago by Aliaksei Holik170 • updated 9 months ago by maduh1710

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