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Use ClinVar submissions file (3/N) #277

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9af35f6
replace clinvar input with selected submissions
pj-sullivan Jan 28, 2026
260e36b
update input arguments
pj-sullivan Jan 30, 2026
8526324
Merge branch 'pj-sullivan/select-submissions' into pj-sullivan/filter…
pj-sullivan Jan 30, 2026
eab7924
Apply code style changes
pj-sullivan Jan 30, 2026
018fed5
clean up testing lines
pj-sullivan Jan 30, 2026
de669a0
remove different versions of 02-annotate
pj-sullivan Feb 2, 2026
1bc3e3d
update run script with edited input files
pj-sullivan Feb 2, 2026
ef54f03
update select_submissions variable in scripts
rjcorb Feb 5, 2026
591e8da
use variant clinsig instead of submission
pj-sullivan Feb 10, 2026
c9655da
update to use variant clinsig
pj-sullivan Feb 19, 2026
dad9ce6
rename resolve clinvar
pj-sullivan Feb 19, 2026
0fd64df
update links to resolve clinvar script
pj-sullivan Feb 19, 2026
da85820
Merge pull request #279 from diskin-lab-chop/pj-sullivan/clinsig
pj-sullivan Feb 23, 2026
b1bfe1f
Apply code style changes
pj-sullivan Feb 23, 2026
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67 changes: 14 additions & 53 deletions run_autogvp.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -15,10 +15,6 @@ variant_summary_file="$BASEDIR/data/ClinVar-selected-submissions.tsv"
# define parameter variables
while [ $# -gt 0 ]; do
case "$1" in
--workflow*|-w*)
if [[ "$1" != *=* ]]; then shift; fi # Value is next arg if no `=`
workflow="${1#*=}"
;;
--vcf*|-v*)
if [[ "$1" != *=* ]]; then shift; fi
vcf_file="${1#*=}"
Expand All @@ -27,10 +23,6 @@ while [ $# -gt 0 ]; do
if [[ "$1" != *=* ]]; then shift; fi
filtering_criteria="${1#*=}"
;;
--clinvar*|-c*)
if [[ "$1" != *=* ]]; then shift; fi
clinvar_file="${1#*=}"
;;
--intervar*|-i*)
if [[ "$1" != *=* ]]; then shift; fi
intervar_file="${1#*=}"
Expand All @@ -51,7 +43,11 @@ while [ $# -gt 0 ]; do
if [[ "$1" != *=* ]]; then shift; fi
out_file="${1#*=}"
;;
--selected_clinvar_submissions*)
--sample_id*|-s*)
if [[ "$1" != *=* ]]; then shift; fi
sample_id="${1#*=}"
;;
--selected_submissions*|-c*)
if [[ "$1" != *=* ]]; then shift; fi
selected_submissions="${1#*=}"
;;
Expand All @@ -76,19 +72,18 @@ while [ $# -gt 0 ]; do
custom_output_cols="${1#*=}"
;;
--help|-h)
echo "Usage: $0 [-w/--workflow] [-v/--vcf <*.vcf*>] [-f/--filter_criteria=<criteria>] [-c/--clinvar <*.vcf>] [-i/--intervar <*.txt.intervar>] [-a/--autopvs1 <*autopvs1*>] [-m/--multianno <*multianno*>] [-o/--out <output>]"
echo "Usage: $0 [-v/--vcf <*.vcf*>] [-f/--filter_criteria=<criteria>] [-i/--intervar <*.txt.intervar>] [-a/--autopvs1 <*autopvs1*>] [-m/--multianno <*multianno*>] [-c/--selected_clinvar_submissions <refs/ClinVar-selected-submissions.tsv>] [-o/--out <output>]"
echo ""
echo "Options:"
echo " -w/--workflow workflow"
echo " -v/--vcf VCF file"
echo " -f/--filter_criteria VCF filtering criteria"
echo " -c/--clinvar ClinVar file"
echo " -i/--intervar Intervar results file"
echo " -a/--autopvs1 Autopvs1 results file"
echo " -m/--multianno ANNOVAR file"
echo " -O/--outdir output directory"
echo " -o/--out output prefix"
echo " --selected_clinvar_submissions ClinVar variant file with conflicts resolved"
echo " -s/--sample_id sample ID to be added to the output file"
echo " -c/--selected_submissions ClinVar variant file with conflicts resolved"
echo " --variant_summary ClinVar variant summary file"
echo " --submission_summary ClinVar submission summary file"
echo " --conceptIDs list of conceptIDs to prioritize submissions for clinvar variant conflict resolution. Will be ignored if selected_clinvar_submissions is provided"
Expand Down Expand Up @@ -122,7 +117,7 @@ if [[ ! -e $selected_submissions ]]; then
submission_summary=$(find data/ -type f -name "submission_summary*")

# if no files found matching pattern, download latest versions from ClinVar
# if [[ -z "$variant_summary" || -z "$submission_summary" ]]
# if [[ -z "$variant_summary" || -z "$submission_summary" ]]
if [[ ! -e "$variant_summary" || ! -e "$submission_summary" ]]
then

Expand Down Expand Up @@ -184,51 +179,17 @@ intervar_input=$out_dir/${out_file}_intervar_filtered.txt
# Run AutoGVP
echo "Running AutoGVP..."

# Run appropriate Rscript based on workflow source (Cavatica vs. custom)
if [[ "$workflow" = "cavatica" ]] ; then

if [[ -f $clinvar_file ]] ; then

# Run AutoGVP from Cavatica workflow with provided clinvar vcf
Rscript $BASEDIR/scripts/02-annotate_variants_CAVATICA_input.R --vcf $autogvp_input \
--clinvar $clinvar_file \
--multianno $multianno_input \
--intervar $intervar_input \
--autopvs1 $autopvs1_input \
--output $out_file \
--outdir $out_dir \
--variant_summary $selected_submissions

else

# Run AutoGVP from Cavatica workflow with clinvar annotation in sample vcf
Rscript $BASEDIR/scripts/02-annotate_variants_CAVATICA_input.R --vcf $autogvp_input \
--multianno $multianno_input \
--intervar $intervar_input \
--autopvs1 $autopvs1_input \
--output $out_file \
--outdir $out_dir \
--variant_summary $selected_submissions

fi

autogvp_output=${out_dir}/${out_file}".cavatica_input.annotations_report.abridged.tsv"

else

# Run AutoGVP from custom workflow
Rscript $BASEDIR/scripts/02-annotate_variants_custom_input.R --vcf $autogvp_input \
--clinvar $clinvar_file \
# Run AutoGVP variant annotation
Rscript $BASEDIR/scripts/02-annotate_variants.R --vcf $autogvp_input \
--clinvar $selected_submissions \
--multianno $multianno_input \
--intervar $intervar_input \
--autopvs1 $autopvs1_input \
--output $out_file \
--outdir $out_dir \
--variant_summary $selected_submissions \
--sample_id $sample_id

autogvp_output=${out_dir}/${out_file}".custom_input.annotations_report.abridged.tsv"

fi
autogvp_output=${out_dir}/${out_file}".annotations_report.abridged.tsv"


# Parse vcf file so that info field values are in distinct columns
Expand Down
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