216
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Troubleshooting Common Issues
= Troubleshooting Common Issues =
= Troubleshooting Common Issues =
== EPACTS installation errors ==
== EPACTS installation errors ==
== Errors when running EPACTS ==
== Errors when running EPACTS ==
=== Rscript execution error: No such file or directory ===
=== Rscript execution error: No such file or directory ===
If you can find Rscript (e.g. /usr/bin/Rscript, /usr/local/bin/Rscript), or if you can re-install the full Rscript, you can simply avoid the problem by setting your environment variable.
If you can find Rscript (e.g. /usr/bin/Rscript, /usr/local/bin/Rscript), or if you can re-install the full Rscript, you can simply avoid the problem by setting your environment variable.
Otherwise, Hyun will modify EPACTS to not requiring this (so you can run R CMD BATCH instead of Rscript).
Otherwise, Hyun will modify EPACTS to not requiring this (so you can run R CMD BATCH instead of Rscript).
=== ERROR: No overlapping IDs between VCF and PED file. Cannot proceed. ===
=== ERROR: No overlapping IDs between VCF and PED file. Cannot proceed. ===
</pre>
</pre>
<br> The genotype information has FORMAT "GT:EC". For the first SNP (chr11:180567) and individual A001, the genotype is 1/1 and dosage is 2.0000. To access the dosages, you must specify the option "-field EC"
<br> The genotype information has FORMAT "GT:EC". For the first SNP (chr11:180567) and individual A001, the genotype is 1/1 and dosage is 2.0000. To access the dosages, you must specify the option "-field EC".
== Results FIle Clarifications: ==
=== 1. How do I code the INDEL variant names and alleles? ===
Please use the variant name and the allele name directly from IMPUTE or minimac. Please do NOT recode variant names or alleles. We will do this step in the analysis for consistency.
ACTION IF YOU HAVE UPLOADED YOUR FILE: If you have recoded your INDEL alleles, please tell us so we can remove your file and let us know when you can reupload with the original variable and allele names.
=== <br>2. The document asks for the number of homozygotes and heterozygotes in case and control. How do I get this from my data? Is this relevant for imputed data? ===
These numbers were relevant to genotyped data but not for imputed data. We didn't intend to ask for this. To retain the same file format between results already submitted and those to be submitted please retain the columns with a "." for the value.
ACTION IF YOU HAVE UPLOADED YOUR FILE: No action. You do not need to redo the file. We will skip these columns.
=== 3. For the "Imputed" variable, what does imputed mean in the context of the data output from MACH and IMPUTE? ===
This is a hold over from the last round of analysis where we asked for results separately from genotyped SNPs and imputed SNPs and wanted to distinguish between the two. We will use r2_hat or info measures to estimate the accuracy of the genotypes. This column will be retained for consistency with files already submitted but should be filled in with "." or "1". It will not be used in the analysis.
ACTION IF YOU HAVE UPLOADED YOUR FILE: No action. You do not need to redo the file. We will skip this column.
