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DepthofCoverage: More rows in output that in target file
I have used the following commands using DepthOfCoverage tool with two different bed files:
java -jar GenomeAnalysisTK.jar -T DepthOfCoverage -R ucsc_hg19.fa -I WT_recalibrated.bam -L coverage_summary.bed -ct 1 -ct 10 -ct 20 -ct 30 -ct 50 -ct 100 -o WT_cov
The line count for the input and output:
$wc -l WT_cov.sample_interval_summary 4988 WT_cov.sample_interval_summary $ wc -l coverage_summary.bed 10585 coverage_summary.bed
In the other case:
java -jar GenomeAnalysisTK.jar -T DepthOfCoverage -R ucsc_hg19.fa -I WT_recalibrated.bam -L exon.bed -ct 1 -ct 10 -ct 20 -ct 30 -ct 50 -ct 100 -o WT_exon
Line count for the input and output:
$ wc -l WT_exon.sample_interval_summary 5065 WT_exon.sample_interval_summary $ wc -l exon.bed 5065 exon.bed
The input in both the cases is of the standard format as shown below:
chr1 6529578 6529755 chr1 6530273 6530442 chr1 6530543 6530721 chr1 6530773 6530980 chr1 6531028 6531730 chr1 6531768 6531914 chr1 6532563 6532713 chr1 6533023 6533273
Could anyone help to interpret the discrepancy between number of target regions in bed file and _interval_summary file in the above two cases?