-BTI and -nsl options not recognised by UG

Hi,
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 \
-nsl \
-o reads.7317.master.vcf

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,
Ester

Best Answer

Answers

  • pdexheimerpdexheimer Member ✭✭✭✭
    edited May 2013

    -nsl doesn't ring a bell for me, but -BTI was an option a long time ago (pre-1.6, maybe?). The available options are here: http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_genotyper_UnifiedGenotyper.html (and the CommandLineGATK page linked therein)

    Edit: Added the link. Whoops

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Ester,

    Those arguments were deprecated a long time ago. Where did you find these listed? Let me know if it was somewhere in our documentation so that I can remove them.

  • ecuencaecuenca Member

    Hi Geraldine,

    I have found it in the GATK 2.4-3.1 pdf guide book:

    The whole script at page 84:
    Genotyping your samples at these sites
    java -Xmx2g -jar dist/GenomeAnalysisTK.jar \
    -T UnifiedGenotyper \
    -R bundle/b37/human_g1k_v37.fasta \
    -I bundle/b37/NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam \
    -alleles:masterAlleles master.vcf \
    -gt_mode GENOTYPE_GIVEN_ALLELES \
    -out_mode EMIT_ALL_SITES \
    -BTI masterAlleles \
    -stand_call_conf 0.0 \
    -glm BOTH \
    -G none \
    -nsl

    but also in many other places:
    "You should always use -BTI alleles, so that the GATK only looks at the sites on the VCF file, speeds up theprocess a lot. (this will soon be added as a default gatk engine mode)"

    So, BTI and nsl are deprecated but the option to generate the sites file to genotype them in all your samples is still working? Or there is a better/newer tool to do the same?
    Is it worth to recall all my samples together from scratch or can I use 4 multi-sample batch called vcfs that I have and apply this step?

    Thanks a lot,
    Ester

  • ecuencaecuenca Member

    Thank you very much Geraldine, it helps a lot!
    Ester

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