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I would like to convert BAM and VCF files to ADAM format.

How do I do that?

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These transformations are quite simple with the adam-submit script packaged with ADAM.

Transformation of BAM files

adam-submit -- transformAlignments sample.bam sample.alignments.adam

Transformation of VCF files

adam-submit -- transformVariants sample.vcf.gz sample.variants.adam
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  • $\begingroup$ Could you provide a link to the package? It seems like it is this repository but I'm not sure. $\endgroup$
    – llrs
    Jun 28 '18 at 7:07

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