When not saving incomplete tilevars, still save hashes/indexes.

[lightning.git] / example-su92l-1kg.sh

diff --git a/example-su92l-1kg.sh b/example-su92l-1kg.sh
index 5de4a4603b50a14398fda298627143739fe83c71..c4e2b543869fa9fa259090ab2995b98f69e72c83 100755 (executable)
--- a/example-su92l-1kg.sh
+++ b/example-su92l-1kg.sh
@@ -19,11 +19,11 @@ genome=$(lightning     ref2genome   -project ${project} -priority ${priority} -r
 fasta=$(lightning      vcf2fasta    -project ${project} -priority ${priority} -ref ${ref_fa} -genome ${genome} -mask=true ${gvcf})                     ; echo fasta=${fasta}
 # fasta=su92l-4zz18-9nq05jifgz7iult
 
-ref37_lib=$(lightning  import       -project ${project} -priority ${priority} -tag-library ${tagset} -skip-ooo=true -output-tiles=true -include-no-calls ${ref37_fa}) ; echo ref37_lib=${ref37_lib}
+ref37_lib=$(lightning  import       -project ${project} -priority ${priority} -tag-library ${tagset} -skip-ooo=true -output-tiles=true -save-incomplete-tiles ${ref37_fa}) ; echo ref37_lib=${ref37_lib}
 # ref37_lib=su92l-4zz18-vnhlv3g6yp1azls/library.gob
 # 539s
 
-ref38_lib=$(lightning  import       -project ${project} -priority ${priority} -tag-library ${tagset} -skip-ooo=true -output-tiles=true -include-no-calls ${ref_fa}) ; echo ref38_lib=${ref38_lib}
+ref38_lib=$(lightning  import       -project ${project} -priority ${priority} -tag-library ${tagset} -skip-ooo=true -output-tiles=true -save-incomplete-tiles ${ref_fa}) ; echo ref38_lib=${ref38_lib}
 # ref38_lib=su92l-4zz18-swebknshfwsvys6/library.gob
 
 unfiltered=$(lightning import       -project ${project} -priority ${priority} -tag-library ${tagset} -skip-ooo=true -output-tiles=true ${fasta})       ; echo unfiltered=${unfiltered}
@@ -37,6 +37,10 @@ exportvcf=$(lightning  export       -project ${project} -priority ${priority} -i
 # exportvcf=su92l-4zz18-gz4svr6zyvipueu/export.csv
 # 5506s
 
+exporthgvs=$(lightning export       -project ${project} -priority ${priority} -i ${merged38} -output-format hgvs -ref /mnt/su92l-4zz18-u77iyyy7cb05xqv/hg38.fa.gz -output-bed hg38.bed) ; echo exporthgvs=${exporthgvs}
+# 
+# 
+
 stats=$(lightning      stats        -project ${project} -priority ${priority} -i ${merged})                                                            ; echo stats=${stats}
 
 filtered=$(lightning   filter       -project ${project} -priority ${priority} -i ${merged} -min-coverage "0.9" -max-variants "30")                     ; echo filtered=${filtered}
@@ -58,3 +62,4 @@ numpy=$(lightning      export-numpy -project ${project} -priority ${priority} -i
 # 6155s
 # pcapy=$(lightning      pca          -project ${project} -priority ${priority} -i ${numpy})                                                             ; echo pcapy=${pcapy}
 comvar=$(lightning     numpy-comvar -project ${project} -priority ${priority} -i ${numpy} -annotations ${numpy%/matrix.npy}/annotations.tsv)           ; echo comvar=${comvar}
+# comvar=su92l-4zz18-s1yhngobdvcoc2e/commonvariants.csv