example-su92l-1kg.sh

   1 #!/bin/bash
   2
   3 go run . build-docker-image
   4 arv keep docker lightning-runtime
   5
   6 project=su92l-j7d0g-jzei0m9yvgauhjf
   7 gvcf=su92l-4zz18-ykpcoea5nisz74f
   8 fasta=su92l-4zz18-s3e6as6uzsoocsb
   9 tags=su92l-4zz18-92bx4zjg5hgs3yc
  10
  11 go run . import       -project ${project} \
  12    -tag-library ~/keep/by_id/${tags}/tagset.fa.gz \
  13    ~/keep/by_id/${fasta}
  14 go run . filter       -project ${project} \
  15    -i ~/keep/by_id/su92l-4zz18-fcyucnod8y4515p/library.gob \
  16    -min-coverage 0.9 -max-variants 30
  17 go run . export-numpy -project ${project} \
  18    -i ~/keep/by_id/su92l-4zz18-l40xcd2l6dmphaj/library.gob
  19 go run . pca          -project ${project} \
  20    -i ~/keep/by_id/su92l-4zz18-i6fzfoxpdh38yk4/library.npy
  21 go run . plot         -project ${project} \
  22    -i ~/keep/by_id/su92l-4zz18-zqfo7qc3tadh6zb/pca.npy \
  23    -labels-csv ~/keep/by_id/${gvcf}/sample_info.csv \
  24    -sample-fasta-dir ~/keep/by_id/${fasta}