UKB_RAP
UKB_RAP copied to clipboard
Running a script over a bunch of vcf files
Hi
I am interested in individual-level WGS vcf files in "/mnt/project/Bulk/DRAGEN WGS/Whole genome variant call files (VCFs) (DRAGEN) [500k release]" for a list of participants in eid.txt.
eid.txt
I want to locate these vcf files so I done as below but I get error
usr@LV19Y7325V dnanexus-upload-agent-1.5.33-osx %
dx ls "/mnt/project/Bulk/DRAGEN WGS/Whole genome variant call files (VCFs) (DRAGEN) [500k release]" VCF/*gz > tempfile.txt ;
zsh: no matches found: VCF/*gz
I tried this command and got error too
usr@LV19Y7325V dnanexus-upload-agent-1.5.33-osx %
for i in `cat eid.txt`; do dx find data --property eid=$i --folder "/mnt/project/Bulk/DRAGEN WGS/Whole genome variant call files (VCFs) (DRAGEN) [500k release]" ; done
cat: eid.txt: No such file or directory
Or, I tried this
usr@LV19Y7325V ~ % dx ls './*.gz*'
dxpy.utils.resolver.ResolutionError: Unable to resolve "*.gz*" to a data object or folder name in '/Bulk/DRAGEN WGS/Whole genome variant call files (VCFs) (DRAGEN) [500k release]'
Please could somebody help me with this?