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Unreported Variant despite high QUAL
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.