ANGSD vs GATK for genotype likelihoods
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5.6 years ago
cetin.m ▴ 50

Hello,

Can anyone please comment on advantages and disadvantages of ANGSD vs GATK for getting genotype likelihoods?

Our samples are low coverage. And our goal is to do imputation after this step.

Any comments greatly appreciated.

angsd gatk genotype likelihoods • 1.7k views
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I am not 100% sure but ANGSD only implements the error model in GATK with "-gl 2" and the samtools one with "-gl 1"

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