I am working on haploid bacterial data and I ran into a limitation of the program that I either can't solve or it would be nice to add a funtion for it in the future. I'll explain the issue:
Let's say I have (low coverage) data that I want to turn into an alternate fasta reference where:
If I want to keep variants where the AD > [threshold] I can't do
because for my sample it could be that the called ALT is getAD.2 and so far I haven't been able to use anything other than a number as an index to getAD.
This would be solved if we could do:
getAD.getGT OR getAD.IndexOfAlleleWithHighestCount
but to my knowledge none of these will work because JEXL will give an error. Maybe extending JEXL java operation to the AD array could fix it? Because even getAD gives an error.
Do you have a solution to this?
PS. I am sorry if this should have been under General Questions
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