I wonder if it is possible to run the gqt commands on remote data by providing urls? as this would solve a big hurdle of data transfers of huge VCF files with thousands of individuals to local servers or systems where gqt is installed. Instead reading the remote file will save a lot of time.
Try 1: vcf.gz and index files are in the ftp path but the GQT is not able to read the “.gqt” file although it looks in the right path as shown below.
$ /gqt/bin/gqt query -i http://share/chr20.vcf.gz -v -d Test.phe.db -p "Phenotype=2" -g "HOM_REF HOM_ALT UNKNOWN" > common.vcf Auto detect failure: GQT file 'http://share/chr20.vcf.gz.gqt' not found
Try2: .gqt file is parsed with the optional parameter -G but now it says Input/output error.
$ /gqt/bin/gqt query -i http://share/shinyTest/chr20.vcf.gz -v -d Test.phe.db -p "Phenotype=2" -g "HOM_REF HOM_ALT UNKNOWN" -G http://share/chr20.vcf.gz.gqt > common.vcf gqt: Cannot open WAHBM file 'http://share/chr20.vcf.gz.gqt': Input/output error
I wonder if it is possible to run the gqt commands on remote data by providing urls? as this would solve a big hurdle of data transfers of huge VCF files with thousands of individuals to local servers or systems where gqt is installed. Instead reading the remote file will save a lot of time.
Try 1: vcf.gz and index files are in the ftp path but the GQT is not able to read the “.gqt” file although it looks in the right path as shown below.
$ /gqt/bin/gqt query -i http://share/chr20.vcf.gz -v -d Test.phe.db -p "Phenotype=2" -g "HOM_REF HOM_ALT UNKNOWN" > common.vcf Auto detect failure: GQT file 'http://share/chr20.vcf.gz.gqt' not foundTry2: .gqt file is parsed with the optional parameter -G but now it says Input/output error.
$ /gqt/bin/gqt query -i http://share/shinyTest/chr20.vcf.gz -v -d Test.phe.db -p "Phenotype=2" -g "HOM_REF HOM_ALT UNKNOWN" -G http://share/chr20.vcf.gz.gqt > common.vcf gqt: Cannot open WAHBM file 'http://share/chr20.vcf.gz.gqt': Input/output error