GATK - Problem

[amathieu]

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

[Chipper]

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

[amathieu]

Thank !!!!