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How to select insertion or deletion from a indels vcf file?
I have a InDels vcf file which contains both insertions and deletions. I would like to select only insertions or only deletions from this InDels vcf file using the following command line.
$ java -jar $GATK -T SelectVariants -R ref_genome/IRGSP.fasta -V indel.vcf -selectType insertion -o insertion.vcf
From this command, I got the following errors-
ERROR A USER ERROR has occurred (version 3.7-0-gcfedb67):
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions https://software.broadinstitute.org/gatk
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR MESSAGE: Could not create module String because an exception of type NullPointerException occurred caused by exception null
Can anyone tell why is this error? Thanks