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Old 03-21-2016, 03:42 AM   #5
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Location: uk

Join Date: Mar 2009
Posts: 667

I think maybe I understand a bit better now.

I think if you are running lobSTR with a paired-end bam file, you need to give it a bam file that has been name-sorted (samtools sort -n) for the -f parameter, because it needs the two reads of a pair to be next to each other in the file.

Later steps, like running allelotype, may need bam files sorted by coordinate, as shown in some of the examples where they sort the bam files that are output from running losSTR.

Hope this makes more sense.
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