#REEOR# importFromGATK# Error in file(file, "rt") : cannot open the connection

[haohui123]

df <-

• importFromGATK(
• file = file,
• highBulk = HighBulk,
• lowBulk = LowBulk,
• chromList = Chroms
• ) Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file 'Yang_et_al_2013.table': No such file or directory

)> #Set sample and file names

HighBulk <- "SRR834931" LowBulk <- "SRR834927" file <- "SNPs_from_GATK.table"

Choose which chromosomes will be included in the analysis (i.e. exclude smaller contigs)

Chroms <- paste0(rep("Chr", 12), 1:12)

Import SNP data from file

df <-

• importFromGATK(
• file = file,
• highBulk = HighBulk,
• lowBulk = LowBulk,
• chromList = Chroms
• ) Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file 'SNPs_from_GATK.table': No such file or directory

[bmansfeld]

Hello, Please read the more detailed instructions in the vignette. https://github.com/bmansfeld/QTLseqr/raw/master/vignettes/QTLseqr.pdf This will explain where to download these trial data. Ben