User: Cindy

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Cindy20
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New User
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2 months, 1 week ago
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2 years, 1 month ago
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Posts by Cindy

<prev • 30 results • page 1 of 3 • next >
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Joint meta in METAL
... I am using METAL to perform a meta-analysis for interaction. On the wiki, it says "The joint meta-analysis method has been implemented though a patch to METAL available from http://www.sph.umich.edu/csg/abecasis/Metal (Metal Documentation)" I could not find the patch in the METAL website. Anyone kno ...
software error written 9 weeks ago by Cindy20 • updated 9 weeks ago by genomax68k
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SNPTEST v2.5.4 for GWAS analysis
... Hi all, I am using SNPTEST V2.5.4 to run GWAS analysis. the method newml gives two P values: wald test P and likelihood P, which are different. Which one I should use? I used Plink to run logistic regression to compare the P values with SNPTEST, the wald-P in PLINK is close to the likelihood P in ...
snp written 4 months ago by Cindy20
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SNPTEST stratification analysis
... Hi all, I used SNPTEST for GWAS analysis stratified by sex, but the results are totally different with and without sex in the cov_names. SNPTEST said "when using -stratify_on, you should (almost) always specify the same variables to -cov_names to allow for a different baseline between strata. In c ...
snp written 4 months ago by Cindy20
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Comment: C: PLINK --score Erroe
... I have checked and found the problem. I used Gtool to convert `.gen` to `.ped` and `.map` which coded genotype as `11`, `12`, `22`, and `00`, while riskProfile uses `T`/`C`/`G`/`A` as named Allele. Is there any way to recode allele to `AA`, `AB`, `BB` and `NN` in my plink data? I only saw it can do ...
written 6 months ago by Cindy20 • updated 5 months ago by RamRS22k
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PLINK Error: No valid entries in --score file.
... Hi all, When I use plink to run `--score` function I got an Error: > No valid entries in --score file. **logfile:** PLINK v1.90b5.3 64-bit (21 Feb 2018) Options in effect: --bfile all --out PRS --score riskProfile.txt Random number seed: 1543012864 32199 MB ...
plink snp written 6 months ago by Cindy20 • updated 5 months ago by Biostar ♦♦ 20
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vcftools filter Allele frequency for polyploid variants
... Hi all, I have vcf files for mitochondrial DNA, which is polyploid. I want to filter out some variants based on the AF. I tried vcftools, it showed not supported. Anyone knows how to do that? Appreciate ahead ...
sequencing written 22 months ago by Cindy20
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picard MarkDuplicates error
... Hi, I have got a wired error from picard. When I run MarkDuplicates for single file, it works. But when I run multiple files, it shows error as following. Is this because too many files? or something wrong with the virtual box? I am running thin on Ubuntu on VM (host: win 10) Exception in threa ...
sequencing written 23 months ago by Cindy20 • updated 23 months ago by genomax68k
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Add head to coverage output for many files
... Hi, all, I used samtools depth to output read depth for all samples, those files have three columns but no head. I want to merge all samples together to calculate the mean read depth and sd, so I need to add sample name as a header before merge them together. When I use echo, it also output ref po ...
sequencing written 23 months ago by Cindy20 • updated 23 months ago by James Ashmore2.6k
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Python error for variant call
... Dear all, I got a error when output VCF file. "in VCFoutput i.INFO['AC'][index] += 1 IndexError: list index out of range" Here is the part where error from: for x in xrange(len(variant[3])): if variant[3] ...
assembly written 23 months ago by Cindy20 • updated 23 months ago by Istvan Albert ♦♦ 80k
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power calculation for target sequencing and survival data
... I am wondering whether there is a tool can used to calculate power for target sequencing in a case-cohort data. I have a case-cohort with target sequencing data. They are all cancer patients with several years of follow up. I will use some cancer biomarkers (continuous or category data) as outcome, ...
sequence written 23 months ago by Cindy20 • updated 23 months ago by Sej Modha4.2k

Latest awards to Cindy

Popular Question 13 months ago, created a question with more than 1,000 views. For How to map the reads from a Bam file to another reference genome????
Popular Question 13 months ago, created a question with more than 1,000 views. For Picard tools samtofastq for a folder
Scholar 2.1 years ago, created an answer that has been accepted. For A: MToolBox.sh: line 173: check_files.py: command not found

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