v0.1.7

brentp · Aug 31, 2022 · 83e45f0 · 83e45f0
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diff --git a/CHANGES.md b/CHANGES.md
@@ -1,5 +1,5 @@
-v0.1.7 (dev)
-============
+v0.1.7 
+======
 + add wiki page and more information about decomposing variants
 + clarify warning on non ACGT (#23)
 + better error messages on missing/bad zip file

diff --git a/paper/small-set.sh b/paper/small-set.sh
@@ -0,0 +1,6 @@
+set -euo pipefail
+ref=/hpc/cog_bioinf/GENOMES.old/1KP_GRCh38/GRCh38_full_analysis_set_plus_decoy_hla.fa
+bcftools csq -l -O u -o - --threads 3 -s - -f $ref -g Homo_sapiens.GRCh38.104.chr.gff3.gz -c CSQ HG001_GRCh38_1_22_v4.2.1_benchmark.bcf \
+| slivar expr --info 'INFO.highest_impact_order < ImpactOrder.missense' -v - --pass-only -o HG001.bad.bcf
+
+echtvar anno -e cadd.v1.6.hg38.zip HG001.bad.bcf HG001.bad.cadd.bcf