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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
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SVTyper Best Practices for Lumpy Output #248

Closed andrewSharo closed 6 years ago

andrewSharo commented 6 years ago

I was curious if there was an update on best practices for using SVTyper on the output from Lumpy. I tried the recommended command: svtyper \
-B sample.bam \ -S sample.splitters.bam \ -i sample.vcf

sample.gt.vcf but received an error message that the -S option has been deprecated. Is there another way I should be passing the split reads to SVTyper?

ryanlayer commented 6 years ago

Just use the sample bam

On Jun 10, 2018, at 5:51 PM, andrewSharo notifications@github.com wrote:

I was curious if there was an update on best practices for using SVTyper on the output from Lumpy. I tried the recommended command: svtyper \ -B sample.bam -S sample.splitters.bam -i sample.vcf

sample.gt.vcf but received an error message that the -S option has been deprecated. Is there another way I should be passing the split reads to SVTyper?

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andrewSharo commented 6 years ago

Good to know, thanks.