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
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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