Unified Genotyper: low-quality genotypes emitted despite -stand_call_conf 30.0 ?

Dear GATK-Team

I am having a problem with UnifiedGenotyper (gatk.2.1-10 and also gatk.1.4-25): When I run the following command, my VCF-file contains many genotypes with very low GQ, despite the parameter -stand_call_conf 30.0. Am I doing something wrong or is there maybe a bug in the code emitting low-quality genotypes despite the -stand_call_conf setting?

The command for gatk.2.1-10 was:
java -Xmx4G -jar /usr/local/gatk.2.1-10/GenomeAnalysisTK.jar -T UnifiedGenotyper -I 16171groupXXIa.bam -I 16172groupXXIa.bam -R ./groupXXI_reference.fa -o GQI13b2SNPs.vcf --output_mode EMIT_VARIANTS_ONLY -stand_call_conf 30.0 -stand_emit_conf 30.0 --min_base_quality_score 20 --genotype_likelihoods_model SNP

For gatk.1.4-25, it was:
-Xmx4G -jar /usr/local/gatk.1.4-25/dist/GenomeAnalysisTK.jar -T UnifiedGenotyper -I 16171groupXXIa.bam -I 16172groupXXIa.bam -R ./groupXXI_reference.fa -o GQI13b2SNPs.vcf --output_mode EMIT_VARIANTS_ONLY -stand_call_conf 30.0 -stand_emit_conf 30.0 --min_base_quality_score 20 --genotype_likelihoods_model SNP -multiallelic

I tried the same without specifying -stand_emit_conf 30.0 -> the result was the same.

Here is an example from the resulting VCF file with a low-quality (GQ=18.06) genotype emitted:
groupXXI 1041752 . T C 207.17 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=42.00;MQ0=0;QD=34.53 GT:AD:DP:GQ:PL ./. 1/1:0,6:6:18.06:240,18,0

Thank you very much in advance for your help
David

Best Answers

Answers

Sign In or Register to comment.