Pileup format

arshiarshi Posts: 7Member
edited August 2012 in Ask the GATK team

I am running Pileup with the verbose option. I have two questions regarding it. (1) Why are all the value in the mapping quality column 0 ? (2)There is another column, not mentioned in the description of pileup, separated by '@'. What does this column mean ?

11 86988 A A D 0 C37@931@1036@0 11 86989 G G D 0 C37@932@1036@0 11 86990 T T B 0 C37@933@1036@0 11 86991 G G D 0 C37@934@1036@0 11 86992 A A B 0 C37@935@1036@0 11 86993 C C C 0 C37@936@1036@0 11 86994 C CCC D=A 0 C37@937@1036@0,38@0@100@0,39@0@100@0

Thanks, Arshi

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