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..