Unreported Variant despite high QUAL
Posted in Ask the GATK team | Last updated on 2012-12-01 02:14:20


Comments (6)

Hello,

I am trying to investigate why a variant (SNP) is not reported in the vcf file when I use the output_mode as "EMIT_VARIANTS_ONLY". However, when I use "EMIT_ALL_SITES" the site shows a very high QUAL score for the variant. Below is the output my region of interest:

17      7578393 .       A       .       11642   .       AN=2;DP=3927;MQ=41.68;MQ0=0     GT:DP   0/0:3927
17      7578394 .       T       A       32767.01        .       AC=1;AF=0.500;AN=2;BaseQRankSum=-15.336;DP=3927;Dels=0.10;FS=261.618;HaplotypeScore=6301.9653;MLEAC=1;MLEAF=0.500;MQ=41.68;MQ0=0;MQRankSum=-0.197;QD=8.34;ReadPosRankSum=0.049;SB=-5.709e+03 GT:AD:DP:GQ:PL  0/1:1588,1922:3526:99:32767,0,32767
17      7578395 .       G       A       984.01  .       AC=1;AF=0.500;AN=2;BaseQRankSum=-18.165;DP=3927;Dels=0.08;FS=2960.660;HaplotypeScore=5221.3579;MLEAC=1;MLEAF=0.500;MQ=41.68;MQ0=0;MQRankSum=1.442;QD=0.25;ReadPosRankSum=1.547;SB=-6.519e-03 GT:AD:DP:GQ:PL  0/1:3218,401:3619:99:1014,0,32767
17      7578396 .       G       .       9145    .       AN=2;DP=3927;MQ=41.68;MQ0=0     GT:DP   0/0:3910
17      7578397 .       T       .       11392   .       AN=2;DP=3927;MQ=41.68;MQ0=0     GT:DP   0/0:3910

The questionable variant is T to A variant at Chr17:7578394 position.

The command I used is:

 java -Xmx4g -jar /usr/local/lib/GenomeAnalysisTK-2.0-35-g2d70733/GenomeAnalysisTK.jar -R human_g1k_v37.fasta -T UnifiedGenotyper -I CL255.ordered.sorted.realigned.bam -o CL255_SNP.vcf --dbsnp dbsnp_135.b37.vcf -stand_call_conf 30 -stand_emit_conf 0 -dcov 5000 -L "17:7,578,336-7,578,451" -out_mode EMIT_ALL_SITES_

I am unable to attach the data since uploading bam seems to be disallowed.

Any help is appreciated. Thanks


Return to top Comment on this article in the forum