I have installed bam-readcount using
git clone --recursive as per the instructions on github.
I am now using the command below to obtain read-count metrics
bam-readcount -q 1 -b 20 -f reference.fasta -l varScan.variants BAM_FILE >varScan.variants.readcounts
However, I get an empty output with a message
Expect library: SX215 in BAM
My bam file has the @RG field (tab-delimited) as follows
@RG ID:SampleID PL:illumina PU:L006 LB:SX215 SM:SampleID
This was added using Picard. Could anyone be knowing what the problem here is? Thanks!