bigger flank reads than expected

[N-damo]

Hi Dr.shiquan:
I am using bamdst to calculate exom sequencing enrichment efficiency. I got the the PF(passing filter) reads on flank region is 6868603, it is greatly bigger than my expected size. bamdst command is bamdst -p S07084713_Regions.bed -f 100 -o sample sample.bam. So I recalculate it step-by-step myself. Firstly I use samtools view to count PF reads on target region:samtools view -c -F 2820 -L S07084713_Regions.bed sample.bamthe result is 10352919. Secondely I added 100bp to my bed file using awk:awk '{print $1,$2-100,$3+100}' S07084713_Regions.bed|tr ' ' '\t' >padded.bed. Then samtools view to count PF reads on target +/- 100 bp :samtools view -c -F 2820 -L padded.bed. the result is 11049703. Reads on flank region is 11049703-10352919=696784, lower one order of magnitude than bamdst result. I guess something was uncorrect in my step-by-step flow, but I do not know how to figure out.By the way, according to the bamdst output result in coverage.report, could I get enrichment efficient on target +/- 100bp by ( Target Reads+flank Reads)/Mapped Reads?
best regards
Li'anLin

[shiquan]

Sorry for the later reply. Did you fix this problem? The reads covered both the target region and the flank region will be count at each term. So at this moment, this kind of reads will be count twice if you add the target reads and flank reads together. You can try to compare the flank reads and samtools view result of the flanked region only.