When using somaticsniper for somatic mutations detection, the result showed that nearly all mutations identified by somaticsniper have Depth of reads supporting variant(s) in normal equal to 0. But when I double check the vcf file provided by the same command, it seems that there is actually some reads supporting variant in normal, which is shown as follows:
In somaticsniper format output: chr1 12888607 A M A 45 88 88 53 42 0 53 837 647 39 56 706 39 37 130 38 56 551 0 0 0
In vcf format output: chr1 12888607 . A C . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:647:263,288,86,10:551,95,0,0:42:.:0:38:53:56:0:. 0/1:0/1:837:329,377,116,15:706,130,0,1:88:.:88:39,39:53:56,37:2:45
I think the reason for this is that the mean mapping quality for variant reads is 0. However, using IGV I can confirm that these variant reads have mapping quality>0 (some of them has high mapping quality).
So what could be the cause of this problem? Is there any difference between the "Mean mapping quality of reads supporting variant(s) in normal" and the mapping quality in bam files?