EPACTS single --interval-list parameter

[Ana Stankovic]

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, the epacts single finishes 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!

[Ana Stankovic]

After including the FileHandle package in the epacts.pm script a new error is shown:

ERROR: Interval size mismatch

I have tried with different BED files, for example setting it for only chromosome 20 or the chromosomes 1..22, X,Y (and with or without MT), and setting it for different region sizes - whole chromosomes or a region that encompasses the variants in the test VCF. 

I have also tried running with --chr parameter set to 20, and also running it without it. 

I have found that the intervalsByBED function always returns `-1`, so the same error is always shown.  

This is the command line:

epacts single --vcf 1000G_exome_chr20_example_softFiltered.calls.vcf.gz --ped 1000G_dummy_pheno.ped --out intevals_test --test b.wald --pheno DISEASE  --cov AGE --cov SEX  --min-maf 0.001 --run 1 --ref human_g1k_v37.fasta.gz --interval-list chr20.bed

Can you tell me what regions BED file should cover and in what exact format it should be in?

Thank you!