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Depth of Coverage - reported only first exon
this is my interval_list
chr1 762095 762275 LINC00115|NR_024321
chr1 762280 762414 LINC00115|NR_024321
chr1 762420 762565 LINC00115|NR_024321
chr1 777259 777349 LOC643837
chr1 777391 777481 LOC643837
chr1 777482 777642 LOC643837
chr1 783061 783151 LOC643837
chr1 792270 792446 LOC643837
chr1 861266 861496 NM_152486|SAMD11
chr1 865582 865787 NM_152486|SAMD11
chr1 866331 866507 NM_152486|SAMD11
and this is the output from the sample_interval_summary
why am I missing two exons?
this is my cmd:
java -Xmx32g -jar /local/apps/gatk/2.5-2-gf57256b/GenomeAnalysisTK.jar
-I sample.bam -R .../genome.fa -T DepthOfCoverage -o jtn
-geneList hg19.tsv -L exons.list
--interval_merging OVERLAPPING_ONLY -l INFO
Thanks for your input!