EPACTS

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Welcome to EPACTS google group!

Please visit http://genome.sph.umich.edu/wiki/EPACTS for detailed information of EPACTS software pipeline.

Feel free to join the group and ask further questions on EPACTS.

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DusanP, cerve...@gmail.com2

Mar 19

Failed to install epacts following "sudo make"

Hi Too late to help probably but maybe someone else can use it: Needed to reinstall everything after

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Failed to install epacts following "sudo make"

Hi Too late to help probably but maybe someone else can use it: Needed to reinstall everything after

Mar 19

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12/8/23

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12/6/23

meharji arumilli, … Fred Boehm13

7/11/23

EPACTS make-group Error

Hello, I read the message stating that EPACTS may not support annovar annotations, but that making

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EPACTS make-group Error

Hello, I read the message stating that EPACTS may not support annovar annotations, but that making

7/11/23

salvi...@gmail.com, Fred Boehm2

5/28/23

group-wise tests differences and references

Did you happen to get a response to these questions? I, too, would like to understand the tests

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group-wise tests differences and references

Did you happen to get a response to these questions? I, too, would like to understand the tests

5/28/23

sandrit...@gmail.com

11/7/22

no single marker results with kinship

Dear All, I have run the kinship matrix command as indicated below and and got the expected out.kinf

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no single marker results with kinship

Dear All, I have run the kinship matrix command as indicated below and and got the expected out.kinf

11/7/22

Dash -, … DusanP6

11/1/22

EPACTS installation issue

Hi all, did anyone manage to solve this issue? Thanks Dusan Le jeudi 4 juin 2020 à 13:41:53 UTC+2,

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EPACTS installation issue

Hi all, did anyone manage to solve this issue? Thanks Dusan Le jeudi 4 juin 2020 à 13:41:53 UTC+2,

11/1/22

Yun-juan Chang

9/14/22

How can I use EPACTS for mycobacterium tuberculosis ?

Can I use this for mycobacterium tuberculosis ? For example, treating the mycobacterium tuberculosis

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How can I use EPACTS for mycobacterium tuberculosis ?

Can I use this for mycobacterium tuberculosis ? For example, treating the mycobacterium tuberculosis

9/14/22

Aditya Yinaganti

6/23/22

EPACTS file

After running the EPACTS file, I am getting the in .epacts.gz file where the last column is score

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EPACTS file

After running the EPACTS file, I am getting the in .epacts.gz file where the last column is score

6/23/22

Samuel Li

6/23/22

Anyone can explain why the ranking and p-value changed like this?

Hi all, I run epacts using the following code with 2 vcfs, one with filter base on CADD score and the

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Anyone can explain why the ranking and p-value changed like this?

Hi all, I run epacts using the following code with 2 vcfs, one with filter base on CADD score and the

6/23/22

Aditya Yinaganti

6/3/22

epactsR issue

I am trying to run EPACTS and I was able to cure the segemtation fault by making the chunks but when

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epactsR issue

I am trying to run EPACTS and I was able to cure the segemtation fault by making the chunks but when

6/3/22

Syed M. Ijlal Haider

6/2/22

memory issues with epacts.

Dear developers. I am struggling to get emmaxCMC run on my multisample called vcf (61000) samples.

unread,

memory issues with epacts.

Dear developers. I am struggling to get emmaxCMC run on my multisample called vcf (61000) samples.

6/2/22

Aditya Yinaganti

5/25/22

Segmentation fault

I have been trying to use EPACTS for single variant test but this error is coming whenever I try to

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Segmentation fault

I have been trying to use EPACTS for single variant test but this error is coming whenever I try to

5/25/22

sandrit...@gmail.com

5/23/22

single marker binary trait with kinship

Hi All, Which option is needed to run a single variant test of a binary trait using kinship ? thanks

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single marker binary trait with kinship

Hi All, Which option is needed to run a single variant test of a binary trait using kinship ? thanks

5/23/22

Syed M. Ijlal Haider

4/27/22

emmaxCMC is super slow

Dear Prof Dr. Kang, I am extremely sorry for bothering you, Actually I am working with panel

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emmaxCMC is super slow

Dear Prof Dr. Kang, I am extremely sorry for bothering you, Actually I am working with panel

4/27/22

Syed M. Ijlal Haider

4/27/22

[W::vcf_parse] INFO 'ANNO' is not defined in the header, assuming Type=String

I am trying to run emmaxCMC on my vcf file which has been annotated by EPACTS. still everytime I run

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[W::vcf_parse] INFO 'ANNO' is not defined in the header, assuming Type=String

I am trying to run emmaxCMC on my vcf file which has been annotated by EPACTS. still everytime I run

4/27/22

Aditya Yinaganti, syednaje...@gmail.com2

4/20/22

EPACTS not working

It seems that you its not installed properly !! May be you removed the package and reinstall it !! On

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EPACTS not working

It seems that you its not installed properly !! May be you removed the package and reinstall it !! On

4/20/22

Ariana Hale

3/30/22

Essential splice site type

Does anyone know what classifies a variant as essential splice site? Is there a range from the exon

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Essential splice site type

Does anyone know what classifies a variant as essential splice site? Is there a range from the exon

3/30/22