hall-lab / fastqtl Goto Github PK
View Code? Open in Web Editor NEWFork of FastQTL for SVs
Home Page: http://fastqtl.sourceforge.net/
License: GNU General Public License v3.0
Fork of FastQTL for SVs
Home Page: http://fastqtl.sourceforge.net/
License: GNU General Public License v3.0
Hi, would you please upload an example VCF file that contains exactly what the program is looking for when it is reading an SV from LUMPY?
So far, I have run LUMPY on my samples, sorted (lsort) and merged (lmerge) using svtools. Once I sort and merge, there is no longer a separate column for each sample genotype. Instead, the sample ID is in column 8 in the ";" separated list.
Does your modified code handle this properly?
I tried running your modified program using one sample genotype per column (as fastQTL traditionally handles SNVs), but it returned NAs for the result. I assume this is because fastQTL failed to properly read the VCF with SVs in it.
An example VCF would really clear up a lot of confusion for me.
Thanks,
Alex
Which GSL version are you using? I have problems with permutation using GSL 2.4.
Edit:
Apparently, the issue is not with GSL but perhaps with my data. The error only occurs with permutation:
Processing gene [OR4F5]
I've tried to run this on Redhat and Ubuntu, using FastQTL-2.184.linux.tgz binary and by compiling myself, as well as the GTEx eQTL Docker image. It always fails at the same point. Any ideas on what could be wrong and how to proceed?
Thank you!
Best,
Heini
Can you please explain in detail the meaning of the following section of the paper
2.2 Finding a candidate QTL per phenotype
For simplicity, we will focus on a single molecular phenotype P quantified in a set of N samples. Let G be the set of genotype dosages at L variant sites located within a cis-window of 6 W Mb of the genomic location of P. To discover the best candidate QTL for P, FastQTL measures Pearson product-moment correlation coefficients between P and all L variants in G, stores the most strongly correlated variant q [ G as candidate QTL, and assesses its significance by calculating a nominal P-value pn with standard significance tests for Pearson correlation. How can this be affected by a test where only one SNP and its LD proxies (r=0.8) is tested. Thanks!
Hi there,
Thanks for making the fastqtl tool. I have been trying to test it for some of my data.
I realised that it requires the sample count in the phenotype bed and the genotype vcf to be exactly the same, as shown here:
Line 55 in 4d03819
and throws an error otherwise.
I was wondering if this could be made slightly more friendly, for example, using only intersecting samples for further analysis.
It is not rare having slightly different numbers of samples in the genotype file and the phenotype file.
Thanks,
Zhihao
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.