User: GabrielMontenegro

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Posts by GabrielMontenegro

<prev • 143 results • page 1 of 15 • next >
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Comment: C: Forcing A1/A2 alleles in PLINK in a VCF phased file
... I just noticed that after using `--ref-allele force` some of the genotypes that were UNPHASED appear as PHASED in the new vcf file. Is there any way to avoid this from happening? ...
written 5 months ago by GabrielMontenegro540
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Exclude sites on the basis of the proportion of missing data using BCFTOOLS
... I want to do something very simple. I want to keep sites that do not have any missing genotypes (i.e. 100% present across all samples). In vcftools I usually do `--max-missing 1.0` as indicated in the manual, but I want to use BCFTOOLS as it is much quicker. However, I cannot find the equivalent fl ...
genome vcf bcftools vcftools written 6 months ago by GabrielMontenegro540
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Comment: C: Estimating LD score in PLINK
... When I add the `--ld-window` parameter with the other commands, I get this message: `Error: Missing --ld-window parameter`. What parameter for `--ld-window` should I use here? Thanks. ...
written 6 months ago by GabrielMontenegro540
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Comment: C: Estimating LD score in PLINK
... Thanks for the quick reply. What `--ld-window` parameter should I use in order to *always* get r2 values between the SNPs that I am extracting with `--extract`? ...
written 6 months ago by GabrielMontenegro540
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Estimating LD score in PLINK
... LD score is defined as the sum of LD r2 between a variant and all the variants in a region. I want to estimate the LD score for an arbitrary numbers of SNPs in a PLINK format dataset that I have. I was simply planning to get the LD between all snps to get the LDscore. I am trying to do this using t ...
ldscore plink ld written 6 months ago by GabrielMontenegro540 • updated 6 months ago by RamRS25k
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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 10 months ago by GabrielMontenegro540
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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 10 months ago by GabrielMontenegro540
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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 10 months ago by GabrielMontenegro540 • updated 10 months ago by Kevin Blighe52k
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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 10 months ago by GabrielMontenegro540
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Comment: C: Remove not polymorphic sites from VCF
... Using v1.9 solved it - Thanks! ...
written 10 months ago by GabrielMontenegro540

Latest awards to GabrielMontenegro

Popular Question 8 weeks ago, created a question with more than 1,000 views. For Subsetting individuals from IMPUTE2 ref files: .hap and .legend
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Subsetting individuals from IMPUTE2 ref files: .hap and .legend
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Teacher 5 months ago, created an answer with at least 3 up-votes. For A: how to get a subset of vcf file for specific SNPs
Popular Question 6 months ago, created a question with more than 1,000 views. For Subsetting individuals from IMPUTE2 ref files: .hap and .legend
Great Question 6 months ago, created a question with more than 5,000 views. For Population-Scaled Recombination Rate
Popular Question 6 months ago, created a question with more than 1,000 views. For Subsetting individuals from IMPUTE2 ref files: .hap and .legend
Appreciated 8 months ago, created a post with more than 5 votes. For A: Interpreting Ldhat Outputs
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Popular Question 20 months ago, created a question with more than 1,000 views. For Getting the function of genes based on gene names
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Popular Question 20 months ago, created a question with more than 1,000 views. For Gene plot similar to LocusZoom

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