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Picard 2.10.2 is now available. As of 2.10.0, Picard supports NovaSeq CBCL data. Download and read release notes at
**GATK4-BETA.2** is here. That's TWO, as in the second beta release. Be sure to read about the known issues before test driving. See Article#9881 to start and for details.

Unified Genotyper quality call

ProtaeusProtaeus Member
edited April 2013 in Ask the GATK team


I am running the unified genotyper in "EMIT_ALL_CONFIDENT_SITES" with the latest version of GATK and am getting some odd quality assignments of 10000030. It is clear that these sites are not very stellar, so I am wondering what is happening to these sites. Any thoughts?

Below is a snippet from one such region, starting with some seemingly "normal" rows and ending with this seemingly odd assessment of quality. Any thoughts? As some background info, this sample is quite different than reference, so not abnormal to have lots of missing regions when aligned against the reference that I used. It is bacterial. Here is the command line that I ran:

GenomeAnalysisTK.jar -T UnifiedGenotyper -dt NONE -I "$i" -R ../../Ref.fasta -baq RECALCULATE -nt 4 -ploidy 1 -out_mode EMIT_ALL_CONFIDENT_SITES -o "$j".vcf -stand_call_conf 100 -stand_emit_conf 100 -mbq 20

Ref  930 .   C   .   102 .   AN=1;DP=2;MQ=150.00;MQ0=0   GT:DP:MLPSAC:MLPSAF 0:2
Ref  931 .   C   .   107 .   AN=1;DP=2;MQ=150.00;MQ0=0   GT:DP:MLPSAC:MLPSAF 0:2
Ref  932 .   T   .   105 .   AN=1;DP=2;MQ=150.00;MQ0=0   GT:DP:MLPSAC:MLPSAF 0:2
Ref  942 .   A   .   10000030    .   DP=1;MQ=150.00;MQ0=0    GT  .
Ref  1109    .   G   .   10000030    .   DP=2;MQ=150.00;MQ0=0    GT  .
Ref  1110    .   A   .   10000030    .   DP=2;MQ=150.00;MQ0=0    GT  .
Ref  1111    .   T   .   10000030    .   DP=2;MQ=150.00;MQ0=0    GT  .
Ref  1112    .   T   .   10000030    .   DP=2;MQ=150.00;MQ0=0    GT  .
Ref  1113    .   T   .   10000030    .   DP=2;MQ=150.00;MQ0=0    GT  .
Ref  1114    .   A   .   10000030    .   DP=2;MQ=150.00;MQ0=0    GT  .
Ref  1115    .   C   .   10000030    .   DP=2;MQ=150.00;MQ0=0    GT  .
Post edited by Geraldine_VdAuwera on


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