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Old 09-26-2011, 04:14 AM   #1
amathieu
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Location: Paris

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Question 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
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Old 09-26-2011, 04:59 AM   #2
Chipper
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It looks like 0.66 % of your alignments have a mapping quality of 255, I don't think it is a problem.
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Old 09-26-2011, 05:23 AM   #3
amathieu
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Thank !!!!
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