Create test set for batch pipeline

broadinstitute / gnomad_local_ancestry

Hail batch pipeline and scripts for local ancestry inference

MIT License

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Create test set for batch pipeline #43

Closed mike-w-wilson closed 3 years ago

mike-w-wilson commented 3 years ago

Create a full set of test contigs using the amr probands within gnomAD trios

mike-w-wilson commented 3 years ago

Test inputs are located in gs://gnomad-batch/mwilson/lai/inputs/

Phasing: gs://gnomad-batch/mwilson/lai/inputs/phasing/gnomad_chr20_5M_10M_5_amr_probands_020121.vcf.bgz gs://gnomad-batch/mwilson/lai/inputs/phasing/gnomad_chr20_5M_10M_5_afr_probands_020121.vcf.bgz gs://gnomad-batch/mwilson/lai/inputs/phasing/test_ref_panel.vcf.bgz

RFMix/XGMix: gs://gnomad-batch/mwilson/lai/inputs/rfmix/genetic_map_hg38.txt gs://gnomad-batch/mwilson/lai/inputs/rfmix/ref_sample_map.tsv