Hi,
I am trying to get a list of all variants that occur in a certain gene. I want to use whole exome sequencing, so .vcf.gz files. When I run Swiss-Army-Knife feeding in the .vcf.gz and .vcf.gz.tbi, and put the command line as "tabix _FILENAME_.vcf.gz "##:##,###,###-##,###,###" | cut -f 1-9 > variantlist.txt", it uploads a blank file named "variant list.txt" into my project. Am I doing something wrong or is there a better alternative?
Thanks!
I understood that this is error with tabix command. For example, I would use -p vcf since default is format gff. See the manual here http://www.htslib.org/doc/tabix.html
Maybe you can try to run in ttyd or cloud workstation to see if your command first or not first.
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To clarify, I have checked https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=837 to make sure the gene of interest is in the file that I include in Swiss-Army-Knife.
I understood that this is error with tabix command. For example, I would use -p vcf since default is format gff. See the manual here http://www.htslib.org/doc/tabix.html
Maybe you can try to run in ttyd or cloud workstation to see if your command first or not first.
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