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ref_base not equal between samples
Hi cpup,
I am using your tool like in the below command and noticed that the ref_base values are not always the same between samples, despite between aligned to the same reference and passing the same genome/annotation. Is there an explanation for this?
samtools mpileup -aa -l annots.bed -f genome.fa my.bam | cpup --strandless --ends --indel > out.txt
Thanks,
Joe
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