ANGSD: Analysis of next generation Sequencing Data

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Genotype Likelihoods

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Genotype likelihoods from alignments

-GL [int]

If your input is sequencing file you can estimate genotype likelhoods from the mapped reads. Four different methods are available.

soapSNP

-GL 0

Samtools

-GL 1

GATK

-GL 2

Kim et al.

-GL 3 Citation Citation

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