high coverage but few genotype calls: possible causes?+
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8.0 years ago
Jautis ▴ 570

Hi,

I have a sample for which I am able to call very few genotype calls (virtually none) compared to other samples in the dataset. This is despite having relatively high total coverage and number of mapped reads.

All samples were digested with Msp1, but the digestion efficiency (proportion of reads starting and/or ending at a Msp1 cut site) does not differ between samples.

What are some potential causes for this and how can I examine what is happening?

genotype calling sequencing SNP • 1.3k views
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Providing some additional info would be helpful. How many reads and what coverage do you mean by high? What organism are you working with? I am assuming you are doing RAD-Seq or something similar?

What software/pipeline are you using? etc

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