Entering edit mode
11.3 years ago
Biostar User
▴
10
Hi all,
is GATK unifiedGenotyper call Indels ? I ran the following command line and got error!
java -jar /software/GATK-1.0.5083/GenomeAnalysisTK.jar -l INFO -R /hg19.fa -T UnifiedGenotyper\
-I chr22_2.bam -stand_call_conf 30 -stand_emit_conf 10 -glm BOTH
-o chr22_GATK_options.vcf
##### ERROR MESSAGE: Invalid argument value '–glm' at position 16.
##### ERROR Invalid argument value 'BOTH' at position 17.
##### ERROR ----------------------------------------------
Thanks ! Sara
