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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
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BAM files must be coordinate sorted #381

Open gneedle1 opened 2 years ago

gneedle1 commented 2 years ago

I keep getting the error of "BAM files must be coordinate sorted", but all my BAMs have an HD tag.

ryanlayer commented 2 years ago

HD does not mean it is in coordinate order. That warning comes up after inspecting the HD tag, so I suspect your HD tag does not say "SO:coordinate"

On Wed, Jun 29, 2022 at 12:39 PM gneedle1 @.***> wrote:

I keep getting the error of "BAM files must be coordinate sorted", but all my BAMs have an HD tag.

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