Hi,
I am using MarkDuplicate.jar of Picard tools to remove duplicate reads. Then I convert bam file to pileup file to extract coverage for each residue. In the middle of that, I have two kinds of bam, bam before MarkDuplicate.jar and bam after MarkDuplicate.jar. I generate pileup file for each bam file by using samtool's pileup. Then I get the coverage for each residue from pileup file. The coverage value is different between bam before MarkDuplicate.jar and bam after MarkDuplicate.jar? I want to use coverage value for CNV analysis, so it is very critical for my analysis. Could you let me know if someone has the same kind of work. Thank you.
I am using MarkDuplicate.jar of Picard tools to remove duplicate reads. Then I convert bam file to pileup file to extract coverage for each residue. In the middle of that, I have two kinds of bam, bam before MarkDuplicate.jar and bam after MarkDuplicate.jar. I generate pileup file for each bam file by using samtool's pileup. Then I get the coverage for each residue from pileup file. The coverage value is different between bam before MarkDuplicate.jar and bam after MarkDuplicate.jar? I want to use coverage value for CNV analysis, so it is very critical for my analysis. Could you let me know if someone has the same kind of work. Thank you.
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