Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
-BTI and -nsl options not recognised by UG
running the Unified genityper for master file with alleles:
java -Xmx30g -jar /GenomeAnalysisTK-2.5-2-gf57256/GenomeAnalysisTK.jar \
-R /hs37d5.fasta \
-T UnifiedGenotyper \
-I /reads.7317.recal.reduced.bam \
-alleles test_master.vcf \
-gt_mode GENOTYPE_GIVEN_ALLELES \
-out_mode EMIT_ALL_SITES \
-stand_call_conf 0.0 \
-glm BOTH \
-BTI alleles \
-G none \
I'm getting the following messages:
ERROR MESSAGE: Argument with name 'BTI' isn't defined.
ERROR MESSAGE: Argument with name 'nsl' isn't defined.
I've also tried with GATK 2.4 and GenomeAnalysisTK-nightly-2013-04-27-ge9bc60e versions but not working.
Any clue about what's happening?
Thanks a lot,