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Old 02-15-2012, 11:30 PM   #1
dnusol
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Location: Spain

Join Date: Jul 2009
Posts: 133
Default help interpreting samtools tview

Hi, I hope someone helps me find out what is going on here. Samtools is giving me a T/G SNP at position chr19:19737915 in two different sampes.

Sample4:
chr19 19737915 . T G 6.2 . DP=55;VDB=0.0784;AF1=0.4999;AC1=1;DP4=4,9,5,0;MQ=55;FQ=8.65;PV4=0.029,0.009,0.0074,1 GT:PLP:SP:GQ 0/1:35,0,216:18:15:36

Sample1:
chr19 19737915 . T G 20 . DP=24;VDB=0.0656;AF1=0.5;AC1=1;DP4=0,2,4,0;MQ=42;FQ=18.9;PV4=0.067,0.011,0,1 GT:PLP:SP:GQ 0/1:50,0,48:6:12:49

Is it the quality too low? I find the alignment rather strange in this region to believe that is actually a true SNP, but seeing that it is happening in two different samples, it makes me wonder.

Thanks,
Dave
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File Type: jpeg s_4_tview_chr19_19737915.jpeg (138.0 KB, 35 views)
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