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Old 02-01-2017, 05:10 AM   #1
cmccabe
Senior Member
 
Location: chicago

Join Date: Jul 2012
Posts: 351
Default annovar multi-thread option syntax error

I am trying to use the muli-threading option in annovar and not having any luck. Both of my attempts below have yielded syntax errors. I am not sure whats wrong or where to place the -thread option. Thank you .

Code:
perl table_annovar.pl -vcfinput file.vcf humandb/ -buildver hg19 -arg '-hgvs',,,,, -remove -protocol IDP.refGene,avsnp147,popfreq_all_20150413,spidex,dbnsfp33a,clinvar_20161128 -operation g,f,f,f,f,f -otherinfo -nastring -thread 8Syntax error

perl table_annovar.pl -vcfinput file.vcf humandb/ -buildver hg19 -arg '-hgvs',,,,, -thread 8 -remove -protocol IDP.refGene,avsnp147,popfreq_all_20150413,spidex,dbnsfp33a,clinvar_20161128 -operation g,f,f,f,f,f -otherinfo -nastring .
Syntax error
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