The frontline support team will be slow on the forum because we are occupied with a GATK Workshop on March 26th and 27th 2019. We will be back and available to answer questions on the forum on March 28th 2019.
DepthOfCoverage multiple samples
I have about 300 bam files (whole-genome sequence) and I'm trying to get the DepthOfCoverage per chomosome.
I'm using a script to submit a job for each chromosome, like that:
java -jar /GenomeAnalysisTK-3.5/GenomeAnalysisTK.jar -T DepthOfCoverage -R 'ref_gen.fa' -I samplesBam.list -L $Chr -o $Chr.DepthCov -nt 30 -omitIntervals -omitSampleSummary -omitLocusTable
The analysis started without problems, but after a while a got an error about "many files opened".
Sorry for not having the output, but I deleted before realise I was going to need them here.
Is there a better way to do that? I've tried sample by sample, but them I'll have 300x34 chromosomes files to get the average manually.