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  • GATK - Problem

    Hi everybody !

    I use GATK since few days and i have a message when i use this command :

    $ java -Xmx4G -jar GenomeAnalysisTK.jar -T DepthOfCoverage -R chr7.fa -I seq.realigned.fixe.bam -o seq_depth_test -L Chr7.bed -omitBaseOutput -ct 10 -ct 20 -ct 30

    I have the message :

    $ 3907 reads were filtered out during traversal out of 589076 total (0.66%)
    $ 3907 reads (0.66% of total) failing UnmappedReadFilter

    Have you got an idea of the problem ?

    Thank

  • #2
    It looks like 0.66 % of your alignments have a mapping quality of 255, I don't think it is a problem.

    Comment


    • #3
      Thank !!!!

      Comment

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