User: GabrielMontenegro

Reputation:
330
Status:
Trusted
Location:
United Kingdom
Last seen:
1 week, 2 days ago
Joined:
3 years, 10 months ago
Email:
j*************@upch.pe

about me

Posts by GabrielMontenegro

<prev • 118 results • page 1 of 12 • next >
0
votes
1
answer
2.2k
views
1
answers
Comment: C: How to interpret XPEHH (recent selection) score?
... Isn't the sign of the XP-EHH score indicative whether the SNP is under selection in your tested or reference population? I thought (depending on how you computed XPEHH) you would only either positive or negative values. From the supp material: > An XP-EHH score is directional: a positive scor ...
written 5 weeks ago by GabrielMontenegro330
0
votes
1
answer
159
views
1
answer
Subsetting individuals in PLINK when IDs contain underscores "_"
... I am working with a VCF dataset and many individuals have IDs including an underscore. I want to subset them using plink, but I keep getting this error: Error: More than two instances of '_' in sample ID. Is there a way for plink to ignore the underscores in those IDs and treat them as a sing ...
plink written 11 weeks ago by GabrielMontenegro330 • updated 11 weeks ago by pfs170
0
votes
1
answer
427
views
1
answers
Comment: C: Forcing A1/A2 alleles in PLINK in a VCF phased file
... Thanks - that worked! ...
written 12 weeks ago by GabrielMontenegro330
0
votes
1
answer
427
views
1
answers
Comment: C: Forcing A1/A2 alleles in PLINK in a VCF phased file
... So then: `... --ref-allele force ancestral_snps.txt 1 2 ...`. Would this work? Thanks again. ...
written 3 months ago by GabrielMontenegro330
0
votes
1
answer
427
views
1
answers
Comment: C: Forcing A1/A2 alleles in PLINK in a VCF phased file
... So if I understand correctly, the `--ref-allele force` will make the specified (in this case ancestral) alleles be changed to 0? I am checking the help page, but I am not sure what this means: `{refcol} {IDcol} {skip}` ? What column numbers would I need to specify? Is it from the VCF or the `ancestr ...
written 3 months ago by GabrielMontenegro330
0
votes
0
answers
288
views
0
answers
Comment: C: Kinship Relatedness using plink
... Check how PI_HAT is computed in PLINK, specially how IBD is calculated. You will then see that this estimates can be affected for instance by admixture/consanguinity. For example, if your population is highly drifted and/or has experienced various bottlenecks (think of Native Americans say) a PI_HAT ...
written 3 months ago by GabrielMontenegro330
0
votes
0
answers
288
views
0
answers
Comment: C: Kinship Relatedness using plink
... I suggest you to check out this previous post: https://www.biostars.org/p/75335/ ...
written 3 months ago by GabrielMontenegro330
5
votes
1
answer
427
views
1
answer
Forcing A1/A2 alleles in PLINK in a VCF phased file
... I have a phased VCF file and I need to change the alleles of the SNPs so that the alleles coded as 0 represent the ancestral state while the alleles coded as 1 represent the derived state. I got a list of ancestral and derive states for my SNPs in my VCF file and I want to change them using PLINK. ...
vcf plink snp written 3 months ago by GabrielMontenegro330
0
votes
3
answers
406
views
3
answers
Comment: C: 1000 genomes PCA for whole genome
... PLINK can handle VCF files. The problem as Sam mentioned is that you will first need to exclude multi-allelic sites. Also, before doing a PCA, you will have to remove SNPs on LD (i.e. prune your data). You can use the `--indep` or `indep-pairwise` function in PLINK too. ...
written 3 months ago by GabrielMontenegro330
0
votes
0
answers
196
views
0
answers
Merging inconsistencies in PLINK
... I am trying to merge two different PLINK files genotyped on the same platform. However, I found some inconsistencies that could not be solved by the `--flip` command. I checked the SNPs that could not be merged after the flip and found this type of problem: File 1: 4 rs10000432 68.93 ...
plink snp written 3 months ago by GabrielMontenegro330 • updated 4 weeks ago by Biostar ♦♦ 20

Latest awards to GabrielMontenegro

Popular Question 18 days ago, created a question with more than 1,000 views. For Getting the function of genes based on gene names
Centurion 6 months ago, created 100 posts.
Popular Question 7 months ago, created a question with more than 1,000 views. For Using Ldhat To Estimate Effective Population Size
Student 7 months ago, asked a question with at least 3 up-votes. For Good books to learn probability distributions
Scholar 9 months ago, created an answer that has been accepted. For A: How to convert input files from PLINK to snp.plotter?
Popular Question 9 months ago, created a question with more than 1,000 views. For Using Ldhat To Estimate Effective Population Size
Popular Question 9 months ago, created a question with more than 1,000 views. For Using Ldhat To Estimate Effective Population Size
Supporter 9 months ago, voted at least 25 times.
Popular Question 12 months ago, created a question with more than 1,000 views. For Changing Build From 37 To 36 In Snp Data
Popular Question 12 months ago, created a question with more than 1,000 views. For Changing Build From 37 To 36 In Snp Data
Popular Question 22 months ago, created a question with more than 1,000 views. For Interpreting Ldhat Outputs
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Using Ldhat To Estimate Effective Population Size
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Changing Build From 37 To 36 In Snp Data
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Population-Scaled Recombination Rate

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1009 users visited in the last hour