Error With Unifiedgenotyper With Option -Glm Both With Gatk During Variant Calling

Question

[ivivek_ngs]

Hi,

I am using the below command for calling the raw variants using GATK(GenomeAnalysisTK-2.3-4-g57ea19f) on the realigned recalibrated bam file after BQSR and PrintReads steps but am getting an error. Command am using is

java -Xmx14g -jar /data/PGP/gmelloni/GenomeAnalysisTK-2.3-4-g57ea19f/GenomeAnalysisTK.jar -T UnifiedGenotyper -R /scratch/GT/vdas/test_exome/exome/hg19.fa -I /scratch/GT/vdas/pietro/exome_seq/results/T_S7999/T_S7999.realigned.recal.bam -L /scratch/GT/vdas/referenceBed/hg19/ss_v4/SureSelect_XT_Human_All_Exon_V4.bed -D /scratch/GT/vdas/test_exome/exome/databases/dbsnp_137.hg19.vcf –glm BOTH -stand_call_conf 50.0 -stand_emit_conf 10.0 -dcov 200 -l INFO -A AlleleBalance -A DepthOfCoverage -A FisherStrand -log /scratch/GT/vdas/pietro/exome_seq/results/T_S7999/T_S7999.GATKvariants.log -o /scratch/GT/vdas/pietro/exome_seq/results/T_S7999/T_S7999.GATKvariants.raw.vcf

Error:

<h5>ERROR MESSAGE: Invalid argument value '???glm' at position 10.</h5> <h5>ERROR Invalid argument value 'BOTH' at position 11.</h5>

I have used this above command earlier while testing my pipeline with a sample from 1000G project with this version of GATK but did not face any error at that time, but am encountering them with my tumor samples. Can anybody give me any suggestions? I have tried checking the posts and the suggestion I see is version compatibility but I have used this version 5 days back with other sample and the same command worked. Can anybody help me out how to get rid of this error? It would be of great help

Answer 1

[Sam]

From what I saw, your comment –glm BOTH, the – seems to differ from the - used in other part such as -l INFO and -A AlleleBalance. Maybe you should just replace the – with - and that should work.

[Jorge Amigo]

just to add that you can use both --genotype_likelihoods_model / -glm (but not --glm, as Sam already indicated), as referenced in the documentation.