Error while running EPACTS Binary Variant Score test

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Toyanji Joseph

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Feb 23, 2021, 4:17:31 AMFeb 23
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Dear Sir/Madam,
 When I run binary single variant score test,
I get an error saying cannot find DISEASE in ped file at epacts.pm line 168. Where as there is a Disease header as 6th column and the disease status is there also. Would you please help me with this? A snapshot is attached for your reference.

Regards

Toyanji Joseph
20210223_144418.jpg

Toyanji Joseph

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Mar 6, 2021, 1:17:28 AMMar 6
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Dear Sir/Madam,
I was able to run a binary variant score test with the example 1000G_exome_chr20_example_softFiltered.calls.vcf.gz. and get results with test_run_epacts.sh. However when I tried with my own data(exome sequencing data). I was not able to get a proper Manhattan plot or qqplot or the zoom plot though some files are getting generated, most of them are empty. Is the reference human_g1k_v37.fasta.gz applicable for exome sequencing too?  Would you please help me troubleshoot this issue. Please find attached the output directory as out8.rar attached here with this mail for your reference

regards

Toyanji Joseph
out8.rar
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