ref_fa=su92l-4zz18-u77iyyy7cb05xqv/hg38.fa.gz
gvcf=${HOME}/keep/by_id/su92l-4zz18-bgyq36m6gctk63q
info=su92l-4zz18-ykpcoea5nisz74f
-tags=su92l-4zz18-92bx4zjg5hgs3yc
+tagset=su92l-4zz18-92bx4zjg5hgs3yc/tagset.fa.gz
genome=$(lightning ref2genome -project ${project} -priority ${priority} -ref ${ref_fa})
fasta=$(lightning vcf2fasta -project ${project} -priority ${priority} -ref ${ref_fa} -genome ${genome} -mask=true ${gvcf})
-unfiltered=$(lightning import -project ${project} -priority ${priority} -tag-library ${tags}/tagset.fa.gz ${fasta})
+unfiltered=$(lightning import -project ${project} -priority ${priority} -tag-library ${tagset} ${fasta})
filtered=$(lightning filter -project ${project} -priority ${priority} -i ${unfiltered} -min-coverage "0.9" -max-variants "30")
numpy=$(lightning export-numpy -project ${project} -priority ${priority} -i ${filtered})
pca=$(lightning pca -project ${project} -priority ${priority} -i ${numpy})