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DepthofCoverage: More rows in output that in target file

meharmehar Member ✭✭
edited November 2014 in Ask the GATK team

Hi,

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?

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