User: Caragh

gravatar for Caragh
Caragh 40
Reputation:
40
Status:
New User
Location:
Ireland
Last seen:
4 months, 2 weeks ago
Joined:
4 years, 6 months ago
Email:
c**************@gmail.com

Posts by Caragh

<prev • 21 results • page 1 of 3 • next >
0
votes
0
answers
311
views
0
answers
Negative values for imputed genotypes on X chromsomes in females
... Hi there, I imputed a set of around ~10k individuals using the sanger imputation server (1000 Genomes Phase 3 with eagle and PBWT). The autosomal data looks perfect - passed QC fine. However, I am was QCing the X chromosome data and I noticed for pretty much all the SNPs in females there is negativ ...
x chromosome X imputation genotypes written 10 months ago by Caragh 40 • updated 8 months ago by Biostar ♦♦ 20
0
votes
1
answer
1.2k
views
1
answers
Comment: C: PLINK heterozygosity - Negative F statistic?
... Thanks for your help Ram! ...
written 12 months ago by Caragh 40
0
votes
0
answers
1.1k
views
0
answers
Comment: C: vcftool negative relatedness values for family members
... Hi Marcus, Did you ever find out if the + - is irrelavent? I'm wondering the same thing! Thanks, Caragh ...
written 13 months ago by Caragh 40
4
votes
1
answer
1.2k
views
1
answer
PLINK heterozygosity - Negative F statistic?
... Hi there, I am running QC on some GWAS data on 48 samples that we are planning to do linkage analysis with. I have run the --het command in PLINK to check for excess heterozygostity and/or consanguinity. For every sample I am getting a negative F statistic, indicating there is more heterozygosity ...
gwas plink heterozygosity written 13 months ago by Caragh 40 • updated 9 months ago by moldach130
1
vote
1
answer
1.2k
views
1
answer
Minimac3 VCF to .gen and .sample format
... Hi there, I imputed some genotype data using the Michigan imputation server and got the output in VCF format. This is the first time I have used this server and I'm struggling to figure out how to handle the data. Is there a way to convert the VCF files into .gen and .sample files whilst retaining ...
imputation minimac3 snp .gen written 16 months ago by Caragh 40 • updated 16 months ago by chrchang5235.0k
0
votes
0
answers
838
views
0
answers
Genomic inflation in genome-wide survival analysis
... Hi there, I have run some genome-wide survival analysis using genipe (which uses a Cox proportional hazards model). I have cleaned for all the normal QC measures (info>0.95, maf>0.05, missingness<0.1, hwe>5e-6, removed related individuals, removed principal component (PC) outliers) and ...
gwas inflation gif survival genomic written 23 months ago by Caragh 40
0
votes
0
answers
724
views
0
answers
SNPTEST Error - core dumped
... Hi there, I am running a GWAS analysis with SNPTEST, SNPTEST runs for about a minute and then stops and memory dumps. I have run this analysis on these exact file previously but I added in an extra covariate to the phenotype file. The error I am getting is as follows: scanning... read chunk [25 ...
gwas snptest written 2.4 years ago by Caragh 40
0
votes
0
answers
778
views
0
answers
Comment: C: Estimation of Recent Shared Ancestry Using ERSA
... Would you be able to shared your syntax? I managed to get ersa1.0 working using their python scripts but the results are still giving me "no_sig_rel" for most of the individuals, despite their PiHAT stating otherwise. ...
written 2.6 years ago by Caragh 40
0
votes
0
answers
778
views
0
answers
Estimation of Recent Shared Ancestry Using ERSA
... Hi there, I am trying to estimate recent shared ancestry using ERSA2.1. However, when I run the below command, I get "no_sig_rel" for all individuals. ersa --segment_files=mydata.match --control_files=ceu.match --output_file=mydata.out --confidence-level 0.8 From PiHAT calculations there doe ...
gwas ibd shared ancestry identity by descent written 2.6 years ago by Caragh 40
0
votes
0
answers
777
views
0
answers
RVTests cmc beta coefficient
... Hi there, I am carrying out rare variant burden analysis on a quantitative trait. I have run this using the cmc method in RVTests, however I need to calculate a beta coefficient for each gene to see the direction of effect. I'm not sure how to go about doing this or even if this can be done for a c ...
rvtests cmc wald burden written 2.7 years ago by Caragh 40 • updated 2 days ago by pampana.akhil0

Latest awards to Caragh

Popular Question 2.6 years ago, created a question with more than 1,000 views. For Running survival analysis using Rplink
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Genome-wide cox regression in R
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: Genome-wide cox regression in R
Scholar 4.5 years ago, created an answer that has been accepted. For A: Genome-wide cox regression in R

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 973 users visited in the last hour