8000 Phasing SVs without --report_readid · Issue #23 · twolinin/longphase · GitHub
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Phasing SVs without --report_readid #23

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agolicz opened this issue Oct 9, 2022 · 1 comment
Open

Phasing SVs without --report_readid #23

agolicz opened this issue Oct 9, 2022 · 1 comment

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@agolicz
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agolicz commented Oct 9, 2022

Hi,
We have some older SVs generated by cuteSV but without the --report_readid. The old mappings no longer exist. We would like to phase using a different set of mappings. Is the absence of --report_readid likely to affect the results?
Best,
Agnieszka
@ythuang0522
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Hi @agolicz, Yes. the read IDs carrying SVs are essential during co-phasing SNPs/SVs. I am afraid you have to recall the SVs. Otherwise, the program can't partition reads into SV- and non-SV groups properly. --Yao-Ting

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