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
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You should use new HaplotypeCaller for indels, since this was used on the last 1000genomes release.
NB: The HaplotypeCaller was not used on the last 1000 Genomes release. They used the last completely open source version.
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
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.
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You seem to be using an older version of GATK. Perhaps -glm is not a valid parameter for that version?
Thanks! yes I download the new version and it works!
closing this question as it's been answered in the comment.