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how does the tools DepthOfCoverage work?

ahdaahda ChinaMember
edited December 2013 in Ask the GATK team

I have used the tool DepthOfCoverage to stat the depth of my BAM file. my script is as below:

java -Xmx4g -jar GenomeAnalysisTK-2.7-4-g6f46d11/GenomeAnalysisTK.jar -R human_g1k_v37.fasta -T DepthOfCoverage -I IonXpress010.bam -o my.depth

But I'm confuse about the result in the *depth file. for example,

> my.depth\n
Locus   Total_Depth     Average_Depth_sample    Depth_for_none\n
**13:32890500**    0    0.00 0\n
13:32890501     30    30.00 30\n

but in my *.bam file, I tried the order below , while the result is 7, which is not same as 0 in my.depth.

samtools view *.bam | awk '$3==13 && $4<=32890500 && $4+length($10)>=32890500'  - |wc \n 
$ 7

Sorry for my poor English.
can anybody meet this problem ? and tell me how the tools works? Thanks a lot..

Post edited by Geraldine_VdAuwera on


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