User: Caragh

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

Posts by Caragh

<prev • 21 results • page 1 of 3 • next >
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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 22 months ago by Caragh 40 • updated 21 months ago by Biostar ♦♦ 20
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Comment: C: PLINK heterozygosity - Negative F statistic?
... Thanks for your help Ram! ...
written 2.1 years ago by Caragh 40
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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 2.2 years ago by Caragh 40
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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 2.2 years ago by Caragh 40 • updated 21 months ago by moldach130
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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 2.4 years ago by Caragh 40 • updated 2.4 years ago by chrchang5236.9k
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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 2.9 years ago by Caragh 40
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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 3.4 years ago by Caragh 40
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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 3.6 years ago by Caragh 40
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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 3.6 years ago by Caragh 40
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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 3.8 years ago by Caragh 40 • updated 12 months ago by pampana.akhil0

Latest awards to Caragh

Popular Question 3.6 years ago, created a question with more than 1,000 views. For Running survival analysis using Rplink
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Genome-wide cox regression in R
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: Genome-wide cox regression in R
Scholar 5.6 years ago, created an answer that has been accepted. For A: Genome-wide cox regression in R

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