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ryanlayer / samplot

Plot structural variant signals from many BAMs and CRAMs
MIT License
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how to obtain read names / co-ordinates to inspect on IGV #185

Open proukakis opened 1 year ago

proukakis commented 1 year ago

Hello, this is great, and apologies if i am missing something obvious. I have CNV calls based on single cell low coverage WGS, with boundaries very imprecise, and trying to find support in bulk Illumina 85x data. eg this is a nice one- but i really want to look at the reads on IGV- could you explain how to get them?. thanks

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proukakis commented 1 year ago

hi, would love some info if possible before we finalise preprint, thanks

jbelyeu commented 1 year ago

This issue is a bit out of scope, relating perhaps more to IGV than to samplot SV review. However, you could clone/fork this repository and add a print statement in the plot function - after the get_read_data() call, to print out the read_data dictionary. Should output the read names that are included in the plot.

proukakis commented 1 year ago

Ok that sounds great, thanks

From: Jon Belyeu @.> Reply to: ryanlayer/samplot @.> Date: Thursday, 3 August 2023 at 23:55 To: ryanlayer/samplot @.> Cc: "Proukakis, Christos" @.>, Author @.***> Subject: Re: [ryanlayer/samplot] how to obtain read names / co-ordinates to inspect on IGV (Issue #185)

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This issue is a bit out of scope, relating perhaps more to IGV than to samplot SV review. However, you could clone/fork this repository and add a print statement in the plot function - after the get_read_data() call, to print out the read_data dictionary. Should output the read names that are included in the plot.

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