-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,