added a way to force the .csv file to be read with linux formatting i…

…n 1_create_(...) step. Should resolve in much less support - not a problem for the R-part of the GRS

1_create_geno_from_vcf.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 snpListFile=$1; shift
 
-cut -d',' -f2,3 $snpListFile | tr ',' '\t' | sort -nk2 > SNP_CHR.tmp
+cat $snpListFile | tr '\r' '\n' | cut -d',' -f2,3 | tr ',' '\t' | sort -nk2 > SNP_CHR.tmp
 for i in {1..22}
 do
     awk -v "chr=$i" '$2==chr {print $1}' SNP_CHR.tmp > geno/$i.snps