bam-readcount skips genomic positions contained in the bedfile
Hi, I am using bam-readcount to calculate the read counts for each base in a list of genomic positions. However, in most of the samples some positions are missing. Is there a way to force the software to show in any case all the positions defined in the bed file? At the moment I am using the following command: bam-readcount -f [ref-file] -l [bed-file] [input-file]
Thank you.
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