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bmansfeld / QTLseqr

QTLseqr is an R package for QTL mapping using NGS Bulk Segregant Analysis

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chromosomes removed without a reason

realgc opened this issue · comments

commented

Hi,
I'm using QTLseqr and when it comes to the step
df <- importFromGATK(file = rawData, highBulk = aBulk, lowBulk = bBulk, chromList = Chroms)
it shows
Removing the following chromosomes: 1, 2, 3, 4, 5
That's all chromosomes I have! Does anyone have any idea why this is happening?

commented

Hi,
Whats stored in your Chroms variable?
If it doesn't exactly match the names of the chromosomes in your data frame then importFromGATK will remove any line which doesn't contain one of the chromosome names supplied to chromList.
If you don't need to exclude any chromosomes then you can leave chromList = NULL which is the default (i.e. you don't need to even write it)
Hope that helps.
Ben

commented

Thanks Ben!
I have solved the issue by deleting the Chroms <- paste0(), and your response also works.
Best,

commented

Great!
Good luck with the rest of your research.