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Old 03-20-2016, 05:42 AM   #2
Senior Member
Location: uk

Join Date: Mar 2009
Posts: 667

The --rg-sample and --rg-lib parameters should be tags with read-group information, not the bam files.

See the lobSTR FAQs for more info.

I think if you start with a bam file rather than fastq files then it should be sorted and indexed. Note that the command line options description for --bampair says that the file should be sorted by name order, 'samtools sort -n'.
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