statgen / epacts Goto Github PK

Please note that passive mode could be used to download the refs in case of difficulties running epacts from within a singularity container.
my $ftp = Net::FTP->new("$hostname", Debug => 0, Passive => 1) or die "Cannot connect to $hostname $@";

Dear Team,

I am trying to figure out the difference between EPACTS and REGENIE (both of them are linear mixture model). I notice recent FinnGen-metablic-association NC paper use EPACTS rather than REGENIE.

https://www.nature.com/articles/s41467-022-29143-5

Thanks.

Shicheng

Hi,

I have a vcf file that is separated by scaffolds on the chr column. so the names of the scaffolds are not ch1, chr2,...
Is there anyway to make epacts make-kin to accept scaffold names as the input for chromosomes?

Thanks.

Hello!

I am running emmax gene-based CMC test on the sample 47,000 participants. The input vcf file includes 1824 variants. The number of individuals is the same kinship, vcf and ped file. However, the analysis is taking more than 2 days. So far no file with association results has been generated, only Makefile, .phe, .ind, .grp , .cov and .reml files and a large .eigr.R file.
I am using epacts version UKBB.chr1.22.emmaxCMC.AC.eigR
Is there any reason why the analysis is taking so long?
Thank you for your help!

Hi,

hope you are doing well, I just wanted to report an issue that the --min-callrate filter is not working at least for the skat-o test. I tried with and without this filter and got the same results however with RAREMETAL got different results. Afterward, I filtered my VCF using bcftools F_MISSING <=0.05 and then ran skat-o test with epacts and got the same results as for RAREMETAL with a call rate of 0.95. so I think the --min-callrate filter in EPACTS does not work.

I am using this version of EPACTS "e4dfca2d79a4c559e654d7bce52bc422b471f923"

Kind Regards,
Haider

HI,

I am actually running "EMMAX-CMC" on gene panel sequencing data from 61000 individuals. Although I am running 40 jobs in parallel but still its been almost 16 days the job is running on the cluster but no results so far. So after having a look into the job I noticed that --run 40 only works till "MAKE Files" but unfortunately p.emmax is not able to do parallelization. I am just curious if this is the limitation of the tool or I did something wrong? I would really appreciate if someone can help me in fixing this issue since its taking so long to get the gene burden results.

epacts-group --vcf $SCRATCH/input.vcf.gz --ped $SCRATCH/input.ped --kin $SCRATCH/kinship/phenotype.kinf --test emmaxCMC --pheno PHENO --groupf $SCRATCH/lof.grp --out $SCRATCH/result/rareLOF --max-maf 0.01 --min-callrate 0.95 --cov Sex --cov PC1 --cov PC2 --cov PC3 --cov PC4 --cov PC5 --cov PC6 --cov PC7 --cov PC8 --cov PC9 --cov PC10 --run 40

Looking forward to hearing from you.

Kind Regards,
Haider

Hi!
I don't understand how I can implement the common+rare skat analysis with the available R script Joint_CommonRare.R

thanks

I am working on the exome aray data (30% common variants and 70% rare variants). When I run EMMAX for the exome array data, it failed. Here is the error message in the log file. I am wondering if the analysis failed because hte exome array snps do not across the whole genome evenly? Thanks!

--test q.emmax

WARNING - "/home/aa_bmi.single.q.emmax.epacts.cmd", line 15: warning: Skipping data file with no valid points
Warning: empty y range [7.30103:7.30103], adjusting to [7.22802:7.37404]

--test emmaxCMC

"/home/aa.gene.emmaxCMC.epacts.cmd", line 15: warning: Skipping data file with no valid points
Warning: empty y range [5.60206:5.60206], adjusting to [5.54604:5.65808]

I am having problems in running Zoom Plot with the pre-release version 3.4.2.
The command line is following:
epacts zoom --pos 20:87662 --prefix _1_20_38_zoomTest --vcf unit_true_1000G_exome_chr20_example_softFiltered.calls.vcf_GRCh38_liftover.vcf.gz
In the attachment is the error log file - job.err.log

The same command line works with the installed 3.3.0 version and with the same files, and a good plot is generated.
/opt/EPACTS/bin/epacts-zoom zoom --pos 20:87662 --prefix _1_20_38_zoomTest --vcf unit_true_1000G_exome_chr20_example_softFiltered.calls.vcf_GRCh38_liftover.vcf

Do you have some insights in the changes in the new release that could cause this problem?
Thank you

I am using EPACTS v3.4.2 and I am trying to run Single Variant Test - q.emmax test. I am using the provided test files.
I am generating the kinship matrix with the epacts make-kin function.
This is the command line:
epacts make-kin --vcf 1000G_exome_chr20_example_softFiltered.calls.anno.vcf.gz --out 37_342.kinf --ped 1000G_dummy_pheno.ped --run 1 --ref human_g1k_v37.fasta

I use this file in the emmax test:
epacts single --vcf /1000G_exome_chr20_example_softFiltered.calls.anno.vcf.gz --ped /1000G_dummy_pheno.ped --out emmax.q.emmax --test q.emmax --pheno DISEASE --cov AGE --cov SEX --run 8 --ref /human_g1k_v37_decoy.fasta --kinf /37_342.kinf

The task fails with the following error log:
job.err-4.log

But, when I use the kinship file created by all the same files and the same command line, but using EPACTS v3.3.0, the Single Variant test (v3.4.2) passes without errors.

Do you have some insights into what could be the reason behind this?
Thank you!

Hi,

I just wanted to point out an error while running epacts-groups with the latest commit "e4dfca2d79a4c559e654d7bce52bc422b471f923" it works fine with single variant test whereas if I use the same vcf with epacts-groups skat-o I run into an error "malformed tbi index". Secondly I have tested the same vcf and tbi file with epact version 3.3.2 commit id "a5209db1b3929c4dd2f15f27ea085edf3a634ee7" it works fine.

Regards,
Haider

Hi !

I want to meta-analyse several epacts score test results using raremetal and therefore try to convert the format of the epacts output to the rvtests format (usable with raremetal).

The score test result of epacts contains the column "V" for the V statistic. Rvtests output however contains SQRT_V_STAT.

Could you please shortly confirm that the epacts column "V" indeed contains values of the V statistic that were NOT applied to sqrt; ie that sqrt(V) equals SQRT_V_STAT from rvtests?

Thanks in advance!

After finally succcesfully compiling EPACTS using G++, GCC 5 on Ubuntu 18.04 I run into the problem of plots not being generated. I tried running test_run_epacts.sh.
All files are being generated properly, except the plots.

It looks like the gnuplot cmd files are not being generated resulting in a
GPL Ghostscript 9.26: Unrecoverable error, exit code 1
Error: /undefined in LTB

Hi all,

I have successfully run the kinship matrix command and got the expected out.kinf file
When using the kinship matrix in single variant association, the analysis runs fine but is not producing any results

epacts single --vcf input.vcf.gz --out SingleSNP_withkinship --ped pedigree.ped --kin out.kinf --pheno mytrait --cov sex --cov age --missing NA --test q.emmax --run 2

any idea?
Thanks

Sandra

Hello, I am having trouble seting the --interval-list parameter for the epacts single function.
In the documentation it is defined as "List of intervals as a unit to perform association in standard BED format (0-based-inclusive-start, 0-based-exclusive-end)", but all the string formats I have tried have resulted in the same error:
Can't locate object method "new" via package "FileHandle" (perhaps you forgot to load "FileHandle"?) at /usr/local/bin/epacts.pm line 653, <PED> line 659.
I have tried adding a BED file as well, and the same error persists.
Without this parameter, theepacts singlefinishes without any problems.
The files I am using are the EPACTS test files and EPACTS version is v3.4.2.

Thank you for the help!

How did you convert the vcf file to the ped file in the given format?

Hi team,

I'm using EAPCTS v 3.3.1 (~/bin/EPACTS/lib/epactsR/DESCRIPTION). There may be a bug with it as analysis is conducted when wrong path/file for kinship is provided with skat-o.

I'm using following command:

epacts group --vcf $file_vcf  \
--kin ~/model1/kinship_epacts_model2  \
--groupf $file_groups --out CHRN_rareSNPs_model2.skat \
--ped $file_ped --max-maf 0.05 \
--pheno Status --cov age --cov MDS1 \
--cov MDS2 --cov MDS3 --cov MDS4 --cov APOE4_status --test skat --skat-o  

~/model1/kinship_epacts_model2 doesn't exist. EPACTS continued with analyses. I would have expected it to stop or crash.

Thanks.

Hi,
Many reviewers ask us to provide marker R2 when we want to publish our results. And how can I get them from emmax results?

Best wishes,
Kun

Any solution?

Hello, I have files run on both GRCh37 and 38 reference and would like to use EPACTS tools to process them.

In the post on the EPACTS Google Group ( here ) the question of tool support for GRCh38 was asked and the answer was given to change the EPACTS/scripts/epacts.pm file.
But modifying the file by hard coding for one or the other is not something that is compatible with my implementation.
Is there another way to achieve compatibility for both references?

Thank you.

Hello
The result of using --linear for plink and lm for epacts,
Each snp has a different p-value value.
Using linear regression, the p-value shouldn't be much different, but is there another reason?

Installing EPACTS in CentOS Linux release 7.9.2009.

The Make step has the following error messages:
make[2]: *** [Makefile:599: pEmmax.o] Error 1
make[2]: Leaving directory '/users/atin/bin/EPACTS_3.2.6/EPACTS-3.2.6/src'
make[1]: *** [Makefile:321: all-recursive] Error 1
make[1]: Leaving directory '/users/atin/bin/EPACTS_3.2.6/EPACTS-3.2.6'
make: *** [Makefile:252: all] Error 2

Please advise a solution.

Thank you

This is only a personal comment from me, but I think it will be useful for new users.

I have tried several times to install through git but failed, after fixing many dependency problems. Finally, this might be the easiest solution. Download this latest package from the author's page (3.2.6, date: 01/07/2019) and install.
http://csg.sph.umich.edu//kang/epacts/download/EPACTS-3.2.6.tar.gz

Dear All,

I am just curious what is the difference between EPACTS version 3.4 and 3.2.6 or 3.3.2, As I was unable to find a proper documentation on versions. I compared results of all these versions I gave the same input files called the same method the result from 3.2.6 and 3.3.2 were exactly the same (and makes more sense according to my data) whereas the result from 3.4 was totally different and doesn't make sense according to my data as well. so I am just curious what is the difference between these versions?

ps. the command I used for all these versions is as follows.

epacts-single --vcf filtered.vcf.gz --ped phenotype.ped --pheno PHENO --test b.glrt --anno --out Single_SNP_Analysis_COmplete --run 2 | tee log.txt

I look forward to hearing from you.

Kind Regards,
Haider

Hi Developers,

Looking the code for the group.b.wcnt test, the weights was weights <- 1/sqrt(NS[vids]*MAF[vids]*(1-MAF[vids])), does this actually should be weights <- 1/sqrt(MAF[vids]*(1-MAF[vids])). As NS[vids] is the number of called samples for each marker, weight by this way will give more weight to high missing rate variant, seems doesn't make sense.

Thank you very much!
Best regards
Wallace

Does EPACTS work with GRCh38 aligned VCFs? I tried using the --ref option and the scripts generated are still using GRCh37 coordinates? Is there a workaround?

epacts single --vcf manta.gcad.duphold.pass.precise.norm.hwe.vcf.gz --ped ../kage_w_head_model1.ped --min-maf 0.01 --min-mac 10 --pheno AD --test b.wald --pass --ref /restricted/projectnb/casa/ref/GRCh38_full_analysis_set_plus_decoy_hla.fa --out test Detected phenotypes with 2 unique values - 0 and 1 - considering them as binary phenotypes... re-encoding them into 1 and 2
Successfully written phenotypes and 0 covariates across 2000 individuals
Processing chromosome 1...
Processing chromosome 2...
Processing chromosome 3...
Processing chromosome 4...
Processing chromosome 5...
Processing chromosome 6...
Processing chromosome 7...
Processing chromosome 8...
Processing chromosome 9...
Processing chromosome 10...
Processing chromosome 11...
Processing chromosome 12...
Processing chromosome 13...
Processing chromosome 14...
Processing chromosome 15...
Processing chromosome 16...
Processing chromosome 17...
Processing chromosome 18...
Processing chromosome 19...
Processing chromosome 20...
Processing chromosome 21...
Processing chromosome 22...
Processing chromosome X...
Processing chromosome Y...
Processing chromosome MT...

When the makefile is run, it does not find the chr1-chr22 regions as it is looking for 1-22,X,Y,MT.

   make -f /rprojectnb2/kageproj/manta/results.epacts/test.Makefile -j [# of parallel jobs]

Or perform sanity checking using the following command:
make -f /rprojectnb2/kageproj/manta/results.epacts/test.Makefile -n
[farrell@scc-hadoop results.epacts]$ make -f /rprojectnb2/kageproj/manta/results.epacts/test.Makefile -j 5
Rscript /share/pkg.7/epacts/2020-01-21_gitfc9c3a4/install/share/EPACTS/epactsSingle.R --vanilla /share/pkg.7/epacts/2020-01-21_gitfc9c3a4/install /rprojectnb2/kageproj/manta/results.epacts/test.phe NULL /rprojectnb2/kageproj/manta/results.epacts/test.ind /rprojectnb2/kageproj/manta/results.epacts/manta.gcad.duphold.pass.precise.norm.hwe.vcf.gz 11:10000001-20000000 /rprojectnb2/kageproj/manta/results.epacts/test.11.10000001.20000000.epacts GT 0.01 1 10 1000000000 0.5 0 TRUE single.b.wald
Rscript /share/pkg.7/epacts/2020-01-21_gitfc9c3a4/install/share/EPACTS/epactsSingle.R --vanilla /share/pkg.7/epacts/2020-01-21_gitfc9c3a4/install /rprojectnb2/kageproj/manta/results.epacts/test.phe NULL /rprojectnb2/kageproj/manta/results.epacts/test.ind /rprojectnb2/kageproj/manta/results.epacts/manta.gcad.duphold.pass.precise.norm.hwe.vcf.gz 11:20000001-30000000 /rprojectnb2/kageproj/manta/results.epacts/test.11.20000001.30000000.epacts GT 0.01 1 10 1000000000 0.5 0 TRUE single.b.wald
Rscript /share/pkg.7/epacts/2020-01-21_gitfc9c3a4/install/share/EPACTS/epactsSingle.R --vanilla /share/pkg.7/epacts/2020-01-21_gitfc9c3a4/install /rprojectnb2/kageproj/manta/results.epacts/test.phe NULL /rprojectnb2/kageproj/manta/results.epacts/test.ind /rprojectnb2/kageproj/manta/results.epacts/manta.gcad.duphold.pass.precise.norm.hwe.vcf.gz 11:30000001-40000000 /rprojectnb2/kageproj/manta/results.epacts/test.11.30000001.40000000.epacts GT 0.01 1 10 1000000000 0.5 0 TRUE single.b.wald
Rscript /share/pkg.7/epacts/2020-01-21_gitfc9c3a4/install/share/EPACTS/epactsSingle.R --vanilla /share/pkg.7/epacts/2020-01-21_gitfc9c3a4/install /rprojectnb2/kageproj/manta/results.epacts/test.phe NULL /rprojectnb2/kageproj/manta/results.epacts/test.ind /rprojectnb2/kageproj/manta/results.epacts/manta.gcad.duphold.pass.precise.norm.hwe.vcf.gz 11:40000001-50000000 /rprojectnb2/kageproj/manta/results.epacts/test.11.40000001.50000000.epacts GT 0.01 1 10 1000000000 0.5 0 TRUE single.b.wald
Rscript /share/pkg.7/epacts/2020-01-21_gitfc9c3a4/install/share/EPACTS/epactsSingle.R --vanilla /share/pkg.7/epacts/2020-01-21_gitfc9c3a4/install /rprojectnb2/kageproj/manta/results.epacts/test.phe NULL /rprojectnb2/kageproj/manta/results.epacts/test.ind /rprojectnb2/kageproj/manta/results.epacts/manta.gcad.duphold.pass.precise.norm.hwe.vcf.gz 11:50000001-60000000 /rprojectnb2/kageproj/manta/results.epacts/test.11.50000001.60000000.epacts GT 0.01 1 10 1000000000 0.5 0 TRUE single.b.wald
Loading required package: epactsR
Loading required package: epactsR
Loading required package: epactsR
Loading required package: epactsR
Loading required package: epactsR

WARNING -

WARNING -
Cannot parse region 11:10000001-20000000.. Returning emptyCannot parse region 11:50000001-60000000.. Returning empty

WARNING -
Cannot parse region 11:30000001-40000000.. Returning empty

WARNING -
Cannot parse region 11:20000001-30000000.. Returning empty

Hi,

I am using the latest EPACTS and managed to solve many dependencies i.e aclocal 1.4 and gcc 5 from EPACTS google mailing list.

I don't have any issue when running the association tests and I see results generated in the top5000 but the pdf files generated for QQ and manhattan plots have no data plotted.
and when every I ran any test I get this error which I am thinking it has something todo with the issue
export GDFONTPATH=/home/daruma/soft/EPACTS/share/EPACTS; export GNUPLOT_FONTPATH=/home/daruma/soft/EPACTS/share/EPACTS; export GNUPLOT_PS_DIR=/home/daruma/soft/EPACTS/share/EPACTS; export PATH=$PATH:/home/daruma/soft/EPACTS/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; gnuplot /media/daruma/sea8/diabetes/results2.gene.kin.skat-o..epacts.cmd export GDFONTPATH=/home/daruma/soft/EPACTS/share/EPACTS; export GNUPLOT_FONTPATH=/home/daruma/soft/EPACTS/share/EPACTS; export GNUPLOT_PS_DIR=/home/daruma/soft/EPACTS/share/EPACTS; export PATH=$PATH:/home/daruma/soft/EPACTS/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; /home/daruma/soft/EPACTS/bin/epstopdf /media/daruma/sea8/diabetes/results2.gene.kin.skat-o..epacts.mh.eps GPL Ghostscript 9.26: Unrecoverable error, exit code 1 Error: /undefined in LTB

I have this is a common thing and there is an easy way to fix it

Thanks

We noticed that for any gene-based test result from EPACTS VT, that the number of individuals carrying variants (Burden_CNT) do not match with the .vnts files.

1. Is this a bug?

2. there a way to extract the individuals and their genotypes that contribute to the gene-based test results (taking phenotype and covariates into account)?

Example:
VT gene burden output
Number of individuals carrying variant in gene GRB14 = 8

#CHROM BEG END MARKER_ID TOT_MARKERS PASS_MARKERS BURDEN_CNT FRAC_WITH_RARE STAT PVALUE R2 DIRECTION OPT_THRES_RAC OPT_FRAC_WITH_RARE
2 164493140 164621279 2:164493140-164621279_GRB14 17 6 8 0.02632 8.3771 0.0101 0.02756 - 1 0.01645

Grepped for GRB14 across all *.epacts.vnts files = 5 ; 3 are missing.
ALSF_slope_VT.12.epacts.vnts:2:164493140-164621279_GRB14 2:164493140_G/A_rs144301087 0.00164 1 1 Sample055253_G1 0/1
ALSF_slope_VT.12.epacts.vnts:2:164493140-164621279_GRB14 2:164508510_C/T 0.00164 1 1 Sample050255_G1 0/1
ALSF_slope_VT.12.epacts.vnts:2:164493140-164621279_GRB14 2:164527109_C/T 0.00169 1 1 Sample050251_G1 0/1
ALSF_slope_VT.12.epacts.vnts:2:164493140-164621279_GRB14 2:164547710_A/G_rs151334452 0.00164 1 1 Sample064223_G1 0/1
ALSF_slope_VT.12.epacts.vnts:2:164493140-164621279_GRB14 2:164547749_C/T_rs201183506 0.00164 1 1 Sample060583_G1 0/1

The meta command does not seem to be available but is listed as a command option....

epacts meta
ERROR: Unknown command meta. Please see the usage below.
Usage:
epacts [command] [options]

 Command:
   help            Print out brief help message
   man             Print the full documentation in man page style
   single          Perform single variant association
   group           Perform groupwise (burden-style) association test
   anno            Annotate a VCF file
   zoom            Create a locus zoom plot from epacts results
   eta            Perform meta-analysis across multiple epacts results
   make-group      Create the group information for gene-based testing
   make-kin        Create a kinship matrix

I think single.b.spa.R does not exist, and single.b.spa2.R,single.b.spa3.R do exist.

This is causing a make failure on Ubuntu 14.04 and 16.04 for me.

Hello everyone,

I have been trying to run a group-wise burden test, but I'm getting the same error over and over again:

epacts group --vcf PPP_new_bial.vcf.gz --ped PPP.ped --max-maf 0.001 --groupf trunc.grp --pheno DISEASE --test skat --skat-o --out trunc.skat --run 2

ERROR: Phenotypes has only one or less unique values (2)

I have tried changing my ped file phenotype code from 1/2 to 0/1 and I've made sure that it's tab delimited. Does anyone have any idea how to fix this?

Hi team,

I'd like to know the version I'm using but none of the following commands help:

epacts --version

epacts -version

epacts -v

epacts --v

epacts man

epacts help

Thanks!

This will be useful when trying different variant filtering strategies without re-generating the VCF files.

Thanks

Dear all,

I am trying to run mmSKAT test using EPACTS. I try this because I saw this post

https://groups.google.com/g/epacts/c/Ruek7rDqwvQ/m/5wB5_NWLEegJ

my code is below:

epacts group
--vcf "/hpcdata/pid/list/USUHS1-EMMAX/wo-moderate/Rare-variant/0.05/Rare-variant-0.05-anno.vcf.gz"
--ped "/hpcdata/pid/list/USUHS1-EMMAX/wo-moderate/kggseq-EPACTS.ped"
--max-maf 0.1 --pheno DISEASE --kin /hpcdata/pid/list/USUHS1-EMMAX/kinship/wo-complex/USUGS1-wo-complex-region.kinf --test mmskat --skat-o --skat-adj --out /hpcdata/pid/list/USUHS1-EMMAX/wo-moderate/Rare-variant/0.05/EPACTS/SKATO-adj/EPACTS-SKAT-wo-MAC-clinical-definition-pLOF
--run 16 --cov Age --cov sex --cov PC1 --cov PC2 --cov PC3 --cov PC4 --cov PC5 --cov PC6 --cov PC7 --cov PC8 --cov PC9 --cov PC10 --cov PC11 --cov PC12 --cov PC13 --cov PC14 --cov PC15 --cov PC16 --cov PC17 --cov PC18 --cov PC19 --cov PC20 --groupf "/hpcdata/pid/list/USUHS1-EMMAX/wo-moderate/Rare-variant/0.05/Rare-variant-0.05-anno-pLOF.group"

However, it returns an error to me (attached)

Would you mind helping me out?

Thank you very much

Samuel Li
Error.txt