EAPCTS runs analysis if wrong kinship is provided

[complexgenome]

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.

[hyunminkang]

Use ~/model1/kinship_epacts_model2.kin instead

Hyun Min Kang, Ph.D. Associate Professor of Biostatistics University of Michigan, Ann Arbor Email : [email protected]

On Tue, Jan 14, 2020 at 10:17 AM Sanjeev [email protected] wrote:

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.

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[complexgenome]

Can you confirm if valid kinship file without .kinf are read or otherwise? I'm running EPACTS with kinship file name, as kinship_epacts_model1 that results me in an overly inflated result.

https://genome.sph.umich.edu/wiki/EPACTS#Single_Variant_EMMAX_Association_Analysis