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software package for integrative genetic association analysis
I am trying to run the DAP on my dataset with the following command:
dap-g -d gene.sbams.dat -p gene.prior -ld_control 0.5 --all -t 4 > output_file
The tool is displaying the "Segmentation fault"
Any help will be appreciated.
Hi Xiaoquan:
Thank you for your tools, it is very great.
Hi,
Does dap-g Individual-level Data "sbam" format support unknown genotype for certain variant in certain sample? Or one MUST impute their genotype matrix before running dap-g?
Best wishes,
Thank you
Hi,
I am encountering a problem when running the code I checked out and compiled today. Any idea what could be the problem?
Best,
Matthias
./dap-g -d_z sample_data/sim.1.zval.dat -d_ld sample_data/sim.1.LD.dat
============ DAP Configuration ============
INPUT
* summary-level data (z-scores and LD matrix)
* number of candidate SNPs: 1001
PROGRAM OPTIONS
* maximum model size allowed [-msize]: 1001 (no restriction)
* LD control threshold [-ld_control]: 0.25
* normalizing constant convergence threshold [-converg_thresh]: 1.00e-02 (log10 scale)
RUN LOG
Model_Size candidates log10(NC)
Segmentation fault (core dumped)
Hi
I am trying to do a fine-mapping for my eQTL and sQTL data, followed by colocalization with GWAS. I am wondering how to make my grid file. I only have one study so I know that I can set phi to zero. However, I do not know how to choose the omega. Is it OK if I just use 0.1, 0.2, 0.4, 0.8, 1.6
as shown in the example?
Thanks
Hi Xiaoquan,
I'm trying to run the example of torus. But the program always gives me the segmentation fault error. I cloned the git repository from https://github.com/xqwen/dap. Both dag-g and torus were compiled successfully. The example of dag-g successfully finished, but torus example failed.
The geuv data were downloaded from http://www-personal.umich.edu/~xwen/dap/data/geuv/.
Any suggestion?
Thanks for your .
The following are the details.
localhost@torus_src~ pwd
/home/wqshi/packages/dap-master/torus_src
localhost@torus_src~ ls
classdef.h controller.o examples geuv.egene.rst geuv.snp.map.gz locus.cc logistic.h main.cc Makefile torus
controller.cc data geuv.annot.gz geuv.gene.map.gz geuv.summary.bf.gz logistic.cc logistic.o main.o README.md
localhost@torus_src~ torus -d geuv.summary.bf.gz --load_bf -smap geuv.snp.map.gz -gmap geuv.gene.map.gz -annot geuv.annot.gz -est -dump_prior gene_prior > geuv.enrichment.est
Segmentation fault (core dumped)
localhost@torus_src~ g++ --version
g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-28)
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
`
Hi!
I was compiling dap and discovered an error in the Makefiles for dap. The libraries are linked with "-L /usr/local/lib" which should be "-L/usr/local/lib" without a space, otherwise the linker won't pick up on the libraries. I installed the GSL libraries in a nonstandard location and linked them like so...
main: main.o controller.o parser.o SSLR.o
g++ -fopenmp -O3 main.o parser.o controller.o SSLR.o -I/apps/gsl-2.4/include/ -L/apps/gsl-2.4/lib -lgsl -lm -lgslcblas -o dap-g
static: main.o controller.o parser.o SSLR.o
g++ -fopenmp -O3 main.o parser.o controller.o SSLR.o -I/apps/gsl-2.4/include/ -L/apps/gsl-2.4/lib -lgsl -lm -lgslcblas -static -o dap-g.static
main.o: main.cc
g++ -I/apps/gsl-2.4/include/ -L/apps/gsl-2.4/lib -lgsl -c -O3 main.cc
parser.o: parser.cc parser.h
g++ -I/apps/gsl-2.4/include/ -L/apps/gsl-2.4/lib -lgsl -c -O3 parser.cc
controller.o: controller.cc controller.h
g++ -c -O3 -fopenmp -I/apps/gsl-2.4/include/ -L/apps/gsl-2.4/lib -lgsl controller.cc
SSLR.o: SSLR.h SSLR.cc
g++ -c -O3 SSLR.cc -I/apps/gsl-2.4/include/ -L/apps/gsl-2.4/lib -lgsl
clean:
rm *.o dap-g
Hi,
I have noticed that when I run any of the DAP-G commands following these instructions with provided test files I get the error code 1. I have all the outputs and everything seems fine, however if I run echo $?
I get the error 1
, even though the previous commands didn't result in any error messages.
I am guessing that this has something to do with the last couple of lines in the main.cc file:
// all done, print all configs
con.print_dap_config();
con.run();
return 1;
Is this behavior expected?
Thank you in advance,
probalica
Hi Xiaoquan,
I'm trying to do a fine-mapping for my sQTL data. I refer to the steps in this document which provides a summary on the processing of GTEx v8 data. And dag-g was compiled successfully. There was an Segmentation fault running my own data.
Command like this:
~/software/dap-master/dap_src/dap-g -d chr9:99960032:99960105:clu_59499:ENSG00000136874.10.sbams.dat -p ENSG00000136874.10.prior -ld_control 0.5 --all -t 1 > chr9:99960032:99960105:clu_59499:ENSG00000136874.10.txt
Any suggestion?
Thanks
Hi,
Is it possible to use DAP-G in sufficient summary statistics mode if a trait I am working with is binary, not quantitative?
If the answer is yes, what should I provide to the input -d_syy
?
Thank you in advance!
probalica
Hi there!
I would need the sources for the binary version1/dap1_src/dap1
, so that the system administrator at my organization can install it on our cluster. Is there any chance of getting it?
I had mixed success using a binary I built from version1/dap_src
as a replacement. Should both of them work similarly for enloc?
Thanks!
Hi Xiaoquan,
Do we have a function/perl script to convert plink to sbams?
Thanks
Shicheng
Hi!
I ran make on the dap_src folder and obtained the dap-g executable.
However, when I ran the following code
dap-g -d_z sample_data/sim.1.zval.dat -d_ld sample_data/sim.1.LD.dat
I got the error of
Error: unknown option "-d_z"
Please advise; Thanks!
Cheers,
Marie
Hi Xiaoquan,
I am wondering can you share the formula to calculate SYY. I get a different value 1527.381 which is different with 515.6
Thanks.
dap-g -t 8 -ld_control 0.25 -converg_thresh 0.01 -d sample_data/sim.1.sbams.dat --dump_summary2
Hi,
from the documentation it does not become entirely clear of LD is to be provided as r (correlation) or r^2. Maybe you could add to your readme how you generate this data for instance with plink (--r or --r2 option)?
Thanks a lot for clarifying.
Best,
Matthias
DAP-G worked well in my project.
I would like to add prior estimated from functional annotation.
Could you please provide some documentation on the file format required for the -p option?
Is the prior a value from 0 to 1 for each variant with 0 indicating low probability of being causal?
Providing an example prior data file would be great too.
Thank you
I am trying to follow the PTWAS tutorial/docs PTWAS_scan#1-ptwas-eqtl-weight-construction and was following through using the sufficient summary statistics (SSS). After this step with DAP-G on SSS there are no instructions or hints for what to do with the output and how to generate weights for this. Is it only possible to generate the eQTL weights using individual level data? If this is the case - how can one generate the sbams format? This does not appear to be documented anywhere, with only an indication of what the sbams file looks like? I would appreciate any advice on generating these eQTL weights if possible please? It would be great to see reproducible command line usage for how exactly PTWAS_scan.weights.hg38.txt.gz.tbi was generated. I think the relevant information available might be here: https://github.com/xqwen/dap/tree/master/gtex_v8_analysis to reproduce - but how might one use this to generate eQTL weights on ones own data (not GTEx v8 data)?
Many thanks
Hi,
I am trying to use dap together with fastenloc. The perl script that summarizes the dap output expects to find cluster level output in the file. However, in my analysis of z-scores, I do not get any clusters (all SNPs are in cluster -1). How could I solve this issue?
Could I tune some parameters to get clusters?
Or, if indeed all SNPs are independent, can the output of cluster information (containing only one SNP) be enforced?
Thanks for your assistance
Best,
Matthias
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