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somatic mutation site REJECT only because of "DBSNP Site"

circlezcirclez Member
edited April 2013 in Ask the GATK team

Dear Kristian Cibulskis,

I run the mutect with "--enable_extended_output". I found that some of the mutations with quite good quality got rejected only because of "DBSNP Site".

As you know, the DBSNP database have included some somatic mutations as well. So I am worried about that the true somatic mutations might be filtered out inappropriately. Do you think it's proper to keep the mutations with the failure_reasons of DBSNP_Site?

For example:
7 55248926 CCAxGTG T C ALK1T ALK1N 0 DBSNP UNCOVERED 0 0.077336 0 0.99254 0 17 1 0 12.199345 12.223447 3.617702 12.500284 0
0.444444 0.136996 0.02 -0.078943 9 5 4 150 130 60 60 0 0 TT 2.708276 0 0 0.000333 -2.296657 -0.575725 0 -0.001303 9 9 0 281 0 0.62965 0.983402 (4,1,4,0) 24.5 14 66 8 46,37,12,9 54,62,70,91 0.996932 0.839312 0.39571 -0.002982 -0.323501 -0.320518 0 DBSNP Site REJECT

Thanks a lot!
Zhou

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