User: Mr Locuace

gravatar for Mr Locuace
Mr Locuace90
Reputation:
90
Status:
Trusted
Location:
Chile
Last seen:
2 weeks, 1 day ago
Joined:
3 years, 7 months ago
Email:
l*******@gmail.com

Molecular biologist by training that recently joined a Human Genomics group.

Posts by Mr Locuace

<prev • 53 results • page 1 of 6 • next >
3
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Convert physical positions from Hg18 to Hg19
... Hello, I have a file like this one (but with thousands of rows): A B C D 994 437756 1 437756 988 204037 1 641793 982 89637 1 731430 976 48461 1 779891 970 30768 1 810659 964 21334 1 831993 A: score B: size of the genomic region in base pairs C: chromosome ...
liftover written 26 days ago by Mr Locuace90 • updated 26 days ago by ATpoint17k
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Phasing genotype likelihood data and merging them with phased genotype calls data.
... I have 3 sets of genotypes: 1. A multiethnic panel of phased 1000G Phase 3 genotypes in IMPUTE2 format (.hap). 2. Genotype likelihoods (GL) for 40 whole-genotypes of a population A in .vcf format (field FORMAT=GL) 3. An array of about 600.000 SNP (30X coverage) from a population B, which is geneti ...
genotype likelihood phasing genotype calls written 8 weeks ago by Mr Locuace90
2
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192
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Plink2. psam file missing in 1000G Phase3
... Hello, here there is a merged file with all 1000G Phase3 chromosomes: https://www.cog-genomics.org/plink/2.0/resources#1kg_phase3 They provide the .pgen.zst, .pvar.zst and unannotated .pvar.zst files, but no -psam.zst file. Is there any way to create a psam file out of the two former files, so I ...
plink2 written 4 months ago by Mr Locuace90 • updated 4 months ago by chrchang5235.2k
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Comment: C: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
... Thanks so much for this tutorial, Kevin !! ...
written 4 months ago by Mr Locuace90
7
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Get all SNPs that are in high linkage disequilibrium (based on D') for a set of SNPs
... Hello, I have phased plink files of a population. I would like to obtain all SNPs that are in high linkage disequilibrium (LD) for a set of 10 SNPs. I know how to do it according to a r2 threshold, but I need to set this threshold according to D' For instance, this script will output all variants i ...
snp plink ld written 4 months ago by Mr Locuace90 • updated 4 months ago by chrchang5235.2k
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Answer: A: How to calculate Hudson's Fst at Population and SNP level?
... https://www.rdocumentation.org/packages/KRIS/versions/1.1.1/topics/fst.each.snp.hudson ...
written 7 months ago by Mr Locuace90
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Comment: A: Converting ms or msms output to PLINK or VCF files
... Hello, I would also like to do this. Is there any more straight forward way to do this rather than using msprime? Many thanks ...
written 7 months ago by Mr Locuace90
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LD pruning before or after phasing for calculating site frequency spectrum?
... I want to calculate the joint-site frequency spectrum (SFS) of 3 populations from phased genotypes generated by Beagle from Plink files). I'd like to know whether it is best to do LD pruning before or after phasing. Also, which LD threshold would be suitable?. I normally remove variants with r2 > ...
snp ld written 9 months ago by Mr Locuace90
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Comment: C: Merge two phased vcf files from 2 pops keeping same ref allele in merged file
... Thank you very much @finswimmer !! ...
written 9 months ago by Mr Locuace90
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Merge two phased vcf files from 2 pops keeping same ref allele in merged file
... Hello, I want to merge 2 vcf files from 2 different human populations. For each population, this is the pipeline that I am using starting with Plink files: 1. Flip strands according to reference genome using snpflip: https://github.com/mdshw5/snp-flip 2. Get vcf files for each chromosome using Plin ...
bcftools plink beagle written 9 months ago by Mr Locuace90

Latest awards to Mr Locuace

Voter 5 weeks ago, voted more than 100 times.
Popular Question 3 months ago, created a question with more than 1,000 views. For Getting derived alleles from alternate/reference allele data
Popular Question 4 months ago, created a question with more than 1,000 views. For Getting derived alleles from alternate/reference allele data
Popular Question 7 months ago, created a question with more than 1,000 views. For Getting derived alleles from alternate/reference allele data
Popular Question 8 months ago, created a question with more than 1,000 views. For Getting derived alleles from alternate/reference allele data
Popular Question 9 months ago, created a question with more than 1,000 views. For Getting derived alleles from alternate/reference allele data
Popular Question 9 months ago, created a question with more than 1,000 views. For Lift over based on physical position from GRCh37 build 137 to GRCh37 build 132
Popular Question 14 months ago, created a question with more than 1,000 views. For Getting derived alleles from alternate/reference allele data
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Reference & alternative alleles extracted from 1000G, Phase 3
Scholar 16 months ago, created an answer that has been accepted. For A: Reference & alternative alleles extracted from 1000G, Phase 3
Supporter 3.0 years ago, voted at least 25 times.
Autobiographer 3.5 years ago, has more than 80 characters in the information field of the user's profile.

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