up

README.md

@@ -17,4 +17,13 @@ sudo apt install cmake libclang-dev
 * (modkit)[https://github.com/nanoporetech/modkit]
 * VEP: cf pandora_lib_variants for VEP install
 * nanomonsv (cf dependencies at github, TODO: use racon)
-###
+
+## Usage
+
+### Use jq for selecting variants:
+
+* Somatic Variants of chrM (25) 
+```
+zcat /data/longreads_basic_pipe/*/diag/somatic_variants.json.gz | \
+jq -L ./jq_filters -C 'include "jq_filters"; [.data[] | select(.position.contig == 25 and n_in_constit <= 1) | format]'
+```

src/README.md

@@ -1,7 +0,0 @@
-== jq for selecting
-
-* Somatic Variants of chrM (25) 
-```
-zcat /data/longreads_basic_pipe/*/diag/somatic_variants.json.gz | \
-jq -L ./jq_filters -C 'include "jq_filters"; [.data[] | select(.position.contig == 25 and n_in_constit <= 1) | format]'
-```