Normally the annotation of a variant file of 100000 variations takes 5 to 10 min. If the process is longer than expected, try to redownload the dbsnp file with the index (new in version 1.514) You should remove the previous dbsnp file or download an other version.
Different reasons can explain that :
- Depending on your system, the time required for IGV to load differs. So if you constat the BAM file never load, launch first IGV prior to the analysis.
- If you try to upload a BAM file present on a distant server you need to upload it into IGV directly on IGV.
- Check if the bai file corresponding to your bam file is present in the same directory.
I'm working on a MAC but when I click on the launch_varaft.sh script my editor text starts but not VarAFT.
To execute the launch_VarAFT.sh script, you should make a right click on the file and select open with "Terminal" application. Select "always open with" to always open your file with the terminal.
I have installed VarAFT, succesfully annotated my files but when I want to perform a analysis, the progress bar loads, disappears but nothing happens. Why ?
There are a bug when the conf file was generated by default. To solve this issue, you should click on "Settings" on the main menu and next click on "Submit" button without perform change.
Without this step the analysis and filter process won't be succesfully ended.
This issue will be resolved in the next release of VarAFT.