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Can GATK accepts more than one bed file while computing depth of coverage?
Group1.BAMfiles.list has three BAM files:
Group1.BED has three BED files:
java -Xmx12g -jar /gatk/GenomeAnalysisTK-3.8.0/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef/GenomeAnalysisTK.jar \
-T DepthOfCoverage \
-R reference_genome.fa \
-I Group1.BAMfiles.list \
-L Group1.BED \
-dt BY_SAMPLE -dcov 5000 -l INFO \
--omitDepthOutputAtEachBase --omitLocusTable \
--minBaseQuality 0 --minMappingQuality 20 \
--start 1 --stop 5000 --nBins 200 \
--includeRefNSites --countType COUNT_FRAGMENTS \