Question: ANGSD vs GATK for genotype likelihoods
gravatar for cetin.m
12 months ago by
cetin.m50 wrote:


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.

ADD COMMENTlink written 12 months ago by cetin.m50

I am not 100% sure but ANGSD only implements the error model in GATK with "-gl 2" and the samtools one with "-gl 1"

ADD REPLYlink written 12 months ago by Gabriel R.2.7k
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