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Old 03-21-2016, 03:18 AM   #4
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Location: uk

Join Date: Mar 2009
Posts: 667

In the end, it shouldn't matter, because anything that is expecting an unsorted bam file will work perfectly well if you give it a sorted bam file (but of course the reverse is not true, and if a program is expecting a sorted bam file it will throw an error if you give it an unsorted bam file).

I agree with you that the lobSTR documentation is confusing and not consistent. I had looked at the 'usage' page, which seems to give different examples than the genotype-calling page you gave the link to. Also in the usage page's definition of parameters, for --bampair it says that you have to give a bam file sorted by name (samtools sort -n), which it doesn't mention anywhere else where it shows examples of sorting the bam files with samtools sort.
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