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Mark Duplicate for Scaffolds #326

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wangshun1121 opened this issue Nov 29, 2017 · 1 comment
Closed

Mark Duplicate for Scaffolds #326

wangshun1121 opened this issue Nov 29, 2017 · 1 comment

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@wangshun1121
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I am trying to call SNPs of Phyllostachys heterocycla, whose genome was assembled to Scaffold level. I mapped reads with bwa men and sorted and indexed bamfiles, then I tried to use sambamba to mark duplicate reads, and I received errors below:

1sambamba-markdup: More than 16383 reference sequences are unsupported

is there any suggestions for this?

sambamba v0.5.9
@pjotrp
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pjotrp commented Nov 29, 2017

Please use the mailing list https://github.com/biod/sambamba#getting-help

@pjotrp pjotrp closed this as completed Nov 29, 2017
@dpryan79 dpryan79 mentioned this issue Aug 28, 2018
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@pjotrp @wangshun1121