GATAK Selec variant
Hi everybody I have run this command and I took this message it would be appreciated if you could help me.
java -Xmx17G -jar /home/masgari/apps/gatk/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar SelectVariants -R home/masgari/hg19/hg19.fa/ -V 1245.marked_duplicates.vcf/ --select-type-to-include SNP/ -O 1245.marked_duplicates _SNP.vcf
A USER ERROR has occurred: Argument select-type-to-include has a bad value: SNP/. 'SNP/' is not a valid value for Type. Allowed values are Possible values: {NO_VARIATION, SNP, MNP, INDEL, SYMBOLIC, MIXED}
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Remove that extra
/at end ofSNP/in your command.Thanks I have removed /, however, I took this message
Looks like you have a space between
duplicatesand_SNP. Please be mindful of your input options.Use
ADD REPLY/ADD COMMENTto keep threads in logical order.Hello daffodil!
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Cheers!
this is the very same kind of error than in your previous question. Please take the time to try to understand what is going wrong.
Really I am so sorry for my simple question I try to learn and I have started gatak pipeline during this month. thanks for your patiants