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amplab / snap

Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
https://www.microsoft.com/en-us/research/project/snap/
Apache License 2.0
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Question: Can aligned and unaligned reads be outputted into separate BAMs? #141

Closed danfulop closed 2 years ago

danfulop commented 2 years ago

Can aligned and unaligned reads be outputted into separate BAMs from a single run of SNAP?

From reading the manual it doesn't seem like the -F and -E flags allow this functionality. Am I missing something? Please advice 😅