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ANGSD / angsd

Program for analysing NGS data.
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Should I downsample to same sequence depth when call snp using ANGSD #634

Open jiangzy26 opened 1 month ago

jiangzy26 commented 1 month ago

Hi, May I ask you a question? My samples have different sequence depth ranging from 2 to 30, should I downsample to the same depth to 2 when using ANGSD to do SNP calling?

Thank you very much

z0on commented 1 month ago

AFAIK downsampling is always a bad idea. Just keep track of your coverage to use as a covariate in downstream analyses.

On Sep 13, 2024, at 9:50 PM, jzy @.***> wrote:

Hi, May I ask you a question? My samples have different sequence depth ranging from 2 to 30, should I downsample to the same depth to 2 when using ANGSD to do SNP calling?

Thank you very much

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