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ryanlayer / samplot

Plot structural variant signals from many BAMs and CRAMs
MIT License
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Why are linked reads not showed in plots? and --ped info #124

Open giuliafrascarelli opened 3 years ago

giuliafrascarelli commented 3 years ago

Thank you for this amazing tool! I have a question about linked reads, I am using samplot vcf with some barley 10X data but the linked reads that should be showed in green are not present in the plots. I am also interested in the --ped flag, do I need a particular ped format file or the one from plink is ok? To show the parents in the plot do they need to be included in code as bam files?

Thank you!

ryanlayer commented 3 years ago

I am not sure about why the linked reads arnt showing. Could it be b/c you are too zoomed in to see other reads from the same molecule?

The plink format is good.

If you add a ped, the subplots will be labeled based on the relationship. You can control the number of samples in each plot with the --min_entries and --max_entries options.

On Tue, Dec 22, 2020 at 8:15 AM Giulia Frascarelli notifications@github.com wrote:

Thank you for this amazing tool! I have a question about linked reads, I am using samplot vcf with some barley 10X data but the linked reads that should be showed in green are not present in the plots. I am also interested in the --ped flag, do I need a particular ped format file or the one from plink is ok? To show the parents in the plot do they need to be included in code as bam files?

Thank you!

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