Hi!
I ran into trouble trying to run the extract_phase_bcftools.sh script. The lines
mkdir -p $prefix
cd $prefix
rm -r *
either delete all the files in my $prefix folder, including the vcf from whatshap, or create a folder that is never used by this script. the script also seems to look for the $iupac_dir folder which is not declared within it nor is it created by earlier scripts.
It seems I'm misunderstanding your folder philosophy here, and otherwise had trouble running the script. A short fix was enough to make it run (and also to generate 2 files per alleles, as the script creates only 1), but other people might run into this problem too.
Thanks a lot - it's been weeks using your workflow and they'd been immensely useful.
Hi!
I ran into trouble trying to run the extract_phase_bcftools.sh script. The lines
mkdir -p $prefix
cd $prefix
rm -r *
either delete all the files in my $prefix folder, including the vcf from whatshap, or create a folder that is never used by this script. the script also seems to look for the $iupac_dir folder which is not declared within it nor is it created by earlier scripts.
It seems I'm misunderstanding your folder philosophy here, and otherwise had trouble running the script. A short fix was enough to make it run (and also to generate 2 files per alleles, as the script creates only 1), but other people might run into this problem too.
Thanks a lot - it's been weeks using your workflow and they'd been immensely useful.