User: GabrielMontenegro

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510
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United Kingdom
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5 years, 1 month ago
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Posts by GabrielMontenegro

<prev • 138 results • page 1 of 14 • next >
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Comment: C: Remove not polymorphic sites from VCF
... @finswimmer have a quick question, will bcftools get the COUNT of the AA or RR genotypes based on the INFO field? Or will it compute the COUNT for all sites? I am applied this filter after merging my dataset with another dataset and I think I am getting weird results. ...
written 5 weeks ago by GabrielMontenegro510
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Comment: C: FATAL ERROR Exhausted system memory (PLINK 1.07)
... I would recommend to use plink 1.9 as it is *MUCH* faster and handles big files better. ...
written 6 weeks ago by GabrielMontenegro510
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Keep variants with 0% missing in VCF
... I want to know if there is a way to keep sites with 0% missing a VCF file. On vcftools I can do: `vcftools --vcf input_file.vcf --max-missing 1.0 --out output_noMissing` Is there a way to do this with BCFTOOLS as it is much faster? ...
vcf bcftools written 6 weeks ago by GabrielMontenegro510 • updated 6 weeks ago by Kevin Blighe39k
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Comment: C: How to explain my QQ-plot result
... Are these the results of an association analysis? It seems that your p-values are inflated, which can arise due to different reasons, more commonly due to unaccounted populations structure. There is a lot of literature on interpreting GWAS results. Maybe start with this? https://www.nature.com/artic ...
written 8 weeks ago by GabrielMontenegro510
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Comment: C: Remove not polymorphic sites from VCF
... Using v1.9 solved it - Thanks! ...
written 8 weeks ago by GabrielMontenegro510
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Comment: C: Remove not polymorphic sites from VCF
... Thanks! Yes, I think that answers my question. I got this error message though: ``the tag "INFO/COUNT" is not defined in the VCF header``. Do you know how to add this info on my vcf? ...
written 8 weeks ago by GabrielMontenegro510
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Comment: C: Remove not polymorphic sites from VCF
... I think if I do minor allele count = 1 , that will remove them as well. Do you know how to do that in bcftools? Thanks. ...
written 8 weeks ago by GabrielMontenegro510
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Comment: C: Remove not polymorphic sites from VCF
... But, I want to keep polymorphic sites. If one ind is REF/REF and all others ALT/ALT, that site is polymorphic, and I would like to keep it. Is there an expression to remove all sites where the frequency of the REF is equal 100% or 0%? That will solve it. ...
written 8 weeks ago by GabrielMontenegro510
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Comment: C: Remove not polymorphic sites from VCF
... So, I will keep all homozygous sites only? That will keep many sites that are not polymorphic then, which is not what I wanted. ...
written 8 weeks ago by GabrielMontenegro510
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Comment: C: Remove not polymorphic sites from VCF
... Wouldn't that keep all heterozygous genotypes? Is there an expression to remove all sites where REF frequency = 1 or ALT frequency = 1? ...
written 8 weeks ago by GabrielMontenegro510

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