Question: (Closed) Gatk Unifiedgenotyper
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gravatar for Biostar User
5.8 years ago by
Biostar User10
Biostar User10 wrote:

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

gatk • 3.6k views
ADD COMMENTlink modified 5.8 years ago by Raony Guimarães860 • written 5.8 years ago by Biostar User10
2

You seem to be using an older version of GATK. Perhaps -glm is not a valid parameter for that version?

ADD REPLYlink written 5.8 years ago by Neilfws48k

Thanks! yes I download the new version and it works!

ADD REPLYlink written 5.8 years ago by Biostar User10

closing this question as it's been answered in the comment.

ADD REPLYlink written 5.8 years ago by Pierre Lindenbaum113k
0
gravatar for Raony Guimarães
5.8 years ago by
Dublin / Ireland
Raony Guimarães860 wrote:

You should use new HaplotypeCaller for indels, since this was used on the last 1000genomes release.

Source: http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_haplotypecaller_HaplotypeCaller.html

ADD COMMENTlink written 5.8 years ago by Raony Guimarães860

NB: The HaplotypeCaller was not used on the last 1000 Genomes release. They used the last completely open source version.

ADD REPLYlink written 5.8 years ago by Erik Garrison2.1k

Soryy, I was reffering to this:

"""We believe the best possible caller in the GATK is the HaplotypeCaller, which combines a local de novo assembler with a more advanced HMM likelihood function than the UnifiedGenotyper. It should produce excellent SNP, MNP, indel, and short SV calls. It should be the go-to calling algorithm for most projects. It is, for example, how we make our Phase II call set for 1000 Genomes."""

I understand now it was not used on last phase I release from 1000genomes.

http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/

My mistake! :D

ADD REPLYlink written 5.8 years ago by Raony Guimarães860

No worries!

A few notes:

Like other local assembly methods, it seems to have much lower sensitivity than alignment-based detection methods. It does have good sensitivity to larger indel alleles, but I haven't seen much validation data on the longer events.

Also, the GATK HaplotypeCaller appears to have lower sensitivity at loci with more than one alternate. This observation is based off of comparisons we did in the 1000G at complex allele-containing loci between different haplotype callers (cortex, platypus, SGA, GATKv2, freebayes). I believe the method is computing phase post-hoc, and also models multiallelic indels as less likely than other methods.

In sum, use multiple approaches, and compare.

ADD REPLYlink written 5.8 years ago by Erik Garrison2.1k
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