We are running sambamba (0.6.8/0.7.0) actively in an automated pipeline. Recently, we have discovered that sambamba will pick up the index file myfile.bam.bai (if it exists) for the file myfile.bam. In our case, this is incorrect, as we have the index stored in myfile.bai.
Is there any way to force sambamba to use a specified index file?
We are running sambamba (0.6.8/0.7.0) actively in an automated pipeline. Recently, we have discovered that sambamba will pick up the index file
myfile.bam.bai(if it exists) for the filemyfile.bam. In our case, this is incorrect, as we have the index stored inmyfile.bai.Is there any way to force sambamba to use a specified index file?