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mcfrith / tandem-genotypes

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Low coverage PB data #3

Closed npatel22526 closed 5 years ago

npatel22526 commented 5 years ago

Hello,

Based on the paper on biorxiv , the tool seems to be working well at 15x coverage. I have few samples sequence with Pacbio at 10x coverage . Do you have any experience with such low coverage data ? If so, how well it works with it and if you have recommended parameters specific to low coverage long reads?

Thanks, Nick

mcfrith commented 5 years ago

Hi Nick

I believe our paper includes a 6X Pacbio dataset (BAFME), which worked OK for us. So I'd recommend just the standard parameters.

For very large repeat expansions, the number of reads covering the whole expansion might be lower than the genome-wide coverage. So low coverage might be a problem for large repeats.

Have a nice day, Martin