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Hi, I'm working with the UnifiedGenotyper walker and I have detected strange values for the QUAL field of some VCF entries in the output files.

Sometimes in the VCF output file, the QUAL value for different vcf entries it is repited, for example, the QUAL values 32729.73 or 2147483609.73 usually appear in the output and not only in my files, because when I have searched on the GATK forum, this value appears in other users posted vcf files related to other questions.

I have tested it with several GATK versions, and in the latests versions these QUAL numbers are extremely high and I have also detected that the value doesn't correspond with the relationship QUAL~QD*DP.

Another strange thing is that for other QUAL values in the VCF file, it is very common that decimal part begins with a seven. i.e : 32729.73

Have you detected this? Is some kind of bug?

I look forward to your response.

I copy some VCF entries with different GATK versions:

Last version (2.7-2):

chr13    32907535    .    C    CT    2147483609.73    .    AC=1;AF=0.500;AN=2;BaseQRankSum=-1.483;DP=1000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.88;MQ0=0;MQRankSum=13.620;QD=33.72;RPA=11,12;RU=T;ReadPosRankSum=-12.065;STR    GT:AD:DP:GQ:PL    0/1:1386,1037:2453:99:9301,0,13130
chr13    32907589    .    G    GT    2147483609.73    .    AC=1;AF=0.500;AN=2;BaseQRankSum=6.991;DP=999;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.93;MQ0=0;MQRankSum=26.910;QD=28.67;RPA=7,8;RU=T;ReadPosRankSum=-2.595;STR    GT:AD:DP:GQ:PL    0/1:1306,1142:2469:99:14116,0,16944

V 2.6-5:

chr13    32907535    .    C    CT    2147483609.73    .    AC=1;AF=0.500;AN=2;BaseQRankSum=-2.106;DP=1000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.81;MQ0=0;MQRankSum=14.984;QD=29.49;RPA=11,12;RU=T;ReadPosRankSum=-9.803;STR    GT:AD:DP:GQ:PL    0/1:1261,1038:2453:99:7901,0,13152
chr13    32907589    .    G    GT    2147483609.73    .    AC=1;AF=0.500;AN=2;BaseQRankSum=6.976;DP=998;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.74;MQ0=0;MQRankSum=25.865;QD=31.47;RPA=7,8;RU=T;ReadPosRankSum=-0.572;STR    GT:AD:DP:GQ:PL    0/1:1184,1142:2469:99:13365,0,16796

V 2.5-2:

chr13    32907535    .    C    CT    32729.73    .    AC=1;AF=0.500;AN=2;BaseQRankSum=0.023;DP=1000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.75;MQ0=0;MQRankSum=-3.054;QD=32.73;RPA=11,12;RU=T;ReadPosRankSum=3.137;STR    GT:AD:DP:GQ:PL    0/1:0,29:2453:99:7901,0,13152
chr13    32907589    .    G    GT    32729.73    .    AC=1;AF=0.500;AN=2;DP=999;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.71;MQ0=0;QD=32.76;RPA=7,8;RU=T;STR    GT:AD:DP:GQ:PL    0/1:0,0:2469:99:13365,0,16796
Comments (1)

I've had the same DNA sample sequenced using two different library prep methods, NEB-Next and Illumina-Nextera, the latter of which generates twice the number of reads than the former. When genotypes for the two samples are called individually using the UnifiedGenotyper, the read depth, DP for the Illumina-Nextera is roughly twice that of the NEB-Next but the quality score, QUAL, remains similar. I was expecting the QUAL to reflect the read depth but obviously this is not the case. Could you enlighten me?