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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 #18

Closed realgc closed 5 years ago

realgc commented 5 years ago

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?

bmansfeld commented 5 years ago

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

realgc commented 5 years ago

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

bmansfeld commented 5 years ago

Great! Good luck with the rest of your research.