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Call ggsashimi to plot converted bams #10

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98477e1
add plot to cram conversion
pj-sullivan Oct 28, 2025
3766496
move plot call outside of cram loop
pj-sullivan Oct 28, 2025
e40872a
fix merge conflicts
pj-sullivan Nov 11, 2025
b41c5f9
update to have more inputs
pj-sullivan Nov 11, 2025
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3 changes: 3 additions & 0 deletions analyses/input/palette.txt
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#e40032
cornflowerblue
#008000
6 changes: 4 additions & 2 deletions analyses/input/test-input.tsv
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Kids_First_Participant_ID cohort_participant_id chr start end ref alt distance source Consequence Hugo_Symbol plot_group broad_histology
PT_JYZA0PNV C95571 chr11 108315911 108315911 G A 0 germline missense_variant&splice_region_variant ATM Low-grade glioma Low-grade astrocytic tumor
PT_BQFM8NH0 C2722113 chr11 44171609 44171609 A G -2 germline splice_acceptor_variant EXT2 Non-neoplastic tumor Benign tumor
PT_40HTPY49 C99753 chr17 31201036 31201036 G A -1 somatic splice_acceptor_variant NF1 DIPG or DMG Diffuse astrocytic and oligodendroglial tumor
PT_TF84B5J9 C3533913 chr1 240801514 240801514 G A -6 somatic splice_region_variant,intron_variant,splice_polypyrimidine_tract_variant RGS7 Oligodendroglioma Diffuse astrocytic and oligodendroglial tumor
PT_RDWE18AC C4114473 chr12 6951966 6951966 C T -17 somatic intron_variant,splice_polypyrimidine_tract_variant PTPN6 Other high-grade glioma Diffuse astrocytic and oligodendroglial tumor
PT_4347ZBEX C216603 chr11 108272506 108272506 A G -26 somatic intron_variant ATM Other high-grade glioma Diffuse astrocytic and oligodendroglial tumor
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1 change: 1 addition & 0 deletions analyses/results/PT_40HTPY49-NF1-chr17:31200036-31202036.tsv
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PT_40HTPY49 bams/663ed64d-47e8-4bec-a0fb-79a61b9574c8-PT_40HTPY49-NF1-chr17:31200036-31202036.bam 663ed64d-47e8-4bec-a0fb-79a61b9574c8
6 changes: 6 additions & 0 deletions analyses/results/PT_4347ZBEX-ATM-chr11:108271506-108273506.tsv
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PT_4347ZBEX bams/1c03b784-4cd1-44a7-a089-d81045ecb7f5-PT_4347ZBEX-ATM-chr11:108271506-108273506.bam 1c03b784-4cd1-44a7-a089-d81045ecb7f5
PT_4347ZBEX bams/8c59e6b4-3553-4ac3-9fbb-2b0ff8225a57-PT_4347ZBEX-ATM-chr11:108271506-108273506.bam 8c59e6b4-3553-4ac3-9fbb-2b0ff8225a57
PT_4347ZBEX bams/0d9c68f8-a507-4a50-b52c-cc4f80a43e61-PT_4347ZBEX-ATM-chr11:108271506-108273506.bam 0d9c68f8-a507-4a50-b52c-cc4f80a43e61
PT_4347ZBEX bams/f1f38907-2974-42a5-a45c-9d3ac1c919df-PT_4347ZBEX-ATM-chr11:108271506-108273506.bam f1f38907-2974-42a5-a45c-9d3ac1c919df
PT_4347ZBEX bams/9aa5f343-bea5-40a5-ad10-fc35b035db2c-PT_4347ZBEX-ATM-chr11:108271506-108273506.bam 9aa5f343-bea5-40a5-ad10-fc35b035db2c
PT_4347ZBEX bams/07db69a8-5f22-4d6c-9b0c-3de147750de9-PT_4347ZBEX-ATM-chr11:108271506-108273506.bam 07db69a8-5f22-4d6c-9b0c-3de147750de9
1 change: 1 addition & 0 deletions analyses/results/PT_RDWE18AC-PTPN6-chr12:6950966-6952966.tsv
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PT_RDWE18AC bams/a511f66a-f51c-48b8-bba4-788f0a4024bb-PT_RDWE18AC-PTPN6-chr12:6950966-6952966.bam a511f66a-f51c-48b8-bba4-788f0a4024bb
1 change: 1 addition & 0 deletions analyses/results/PT_TF84B5J9-RGS7-chr1:240800514-240802514.tsv
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PT_TF84B5J9 bams/8c898407-550a-4a12-8e02-70d3837475d5-PT_TF84B5J9-RGS7-chr1:240800514-240802514.bam 8c898407-550a-4a12-8e02-70d3837475d5
22 changes: 18 additions & 4 deletions analyses/results/bams/md5sum.txt
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@@ -1,4 +1,18 @@
b813cb028bbacb56f7e86146dfcec3a2 results/bams/49629206-ef0a-4636-83cf-b37021e60def-PT_JYZA0PNV-ATM-chr11:108305911-108325911.bam
881cf3a5cf83ff062256184f072c5ca9 results/bams/49629206-ef0a-4636-83cf-b37021e60def-PT_JYZA0PNV-ATM-chr11:108305911-108325911.bam.bai
cd15f9a0ca11bf83e2682325004f031e results/bams/ccc08827-804f-4966-95bd-8fc960e45093-PT_BQFM8NH0-EXT2-chr11:44161609-44181609.bam
d3cb164ed575c1859886acac74ba6183 results/bams/ccc08827-804f-4966-95bd-8fc960e45093-PT_BQFM8NH0-EXT2-chr11:44161609-44181609.bam.bai
f62bf553c3db2b9fb144df554477489d results/bams/07db69a8-5f22-4d6c-9b0c-3de147750de9-PT_4347ZBEX-ATM-chr11:108271506-108273506.bam
4f3e4ca851c4355d4035a3175c905a3c results/bams/07db69a8-5f22-4d6c-9b0c-3de147750de9-PT_4347ZBEX-ATM-chr11:108271506-108273506.bam.bai
9b6df5998f8788ae28a7daa3fd6c5bf8 results/bams/0d9c68f8-a507-4a50-b52c-cc4f80a43e61-PT_4347ZBEX-ATM-chr11:108271506-108273506.bam
25b4296848b1ce76e59176dd539d74e4 results/bams/0d9c68f8-a507-4a50-b52c-cc4f80a43e61-PT_4347ZBEX-ATM-chr11:108271506-108273506.bam.bai
70dd448523195a0eb2bfc5548da7ee1b results/bams/1c03b784-4cd1-44a7-a089-d81045ecb7f5-PT_4347ZBEX-ATM-chr11:108271506-108273506.bam
0fa550bdf250cc6992e39cce08296ba5 results/bams/1c03b784-4cd1-44a7-a089-d81045ecb7f5-PT_4347ZBEX-ATM-chr11:108271506-108273506.bam.bai
0c037b4944eeb7ebb98fed6783c6fc6a results/bams/663ed64d-47e8-4bec-a0fb-79a61b9574c8-PT_40HTPY49-NF1-chr17:31200036-31202036.bam
1c4217a69be28488abafd02f7011cc6e results/bams/663ed64d-47e8-4bec-a0fb-79a61b9574c8-PT_40HTPY49-NF1-chr17:31200036-31202036.bam.bai
0d0489d210a8380b56472aea82a47ffb results/bams/8c59e6b4-3553-4ac3-9fbb-2b0ff8225a57-PT_4347ZBEX-ATM-chr11:108271506-108273506.bam
12068a3499bebeb97b0ddaad92743536 results/bams/8c59e6b4-3553-4ac3-9fbb-2b0ff8225a57-PT_4347ZBEX-ATM-chr11:108271506-108273506.bam.bai
123959c5f584da5df0fa7b223496e262 results/bams/8c898407-550a-4a12-8e02-70d3837475d5-PT_TF84B5J9-RGS7-chr1:240800514-240802514.bam
75c68e7eadb2ca948fc4b39d65dcf873 results/bams/8c898407-550a-4a12-8e02-70d3837475d5-PT_TF84B5J9-RGS7-chr1:240800514-240802514.bam.bai
0ed8b395e9181ba5774c6a42c09e3819 results/bams/9aa5f343-bea5-40a5-ad10-fc35b035db2c-PT_4347ZBEX-ATM-chr11:108271506-108273506.bam
cbb569ea87983495397ff0a577453036 results/bams/9aa5f343-bea5-40a5-ad10-fc35b035db2c-PT_4347ZBEX-ATM-chr11:108271506-108273506.bam.bai
0fd43e5e8a0391bec1e0c8c3f502d3e7 results/bams/a511f66a-f51c-48b8-bba4-788f0a4024bb-PT_RDWE18AC-PTPN6-chr12:6950966-6952966.bam
17cdd453ac057423c953502cb398845e results/bams/a511f66a-f51c-48b8-bba4-788f0a4024bb-PT_RDWE18AC-PTPN6-chr12:6950966-6952966.bam.bai
98868b9270b6fad2736bdf78aaac9a59 results/bams/f1f38907-2974-42a5-a45c-9d3ac1c919df-PT_4347ZBEX-ATM-chr11:108271506-108273506.bam
5f4c6b31d9d67fd23772195a7254eb1c results/bams/f1f38907-2974-42a5-a45c-9d3ac1c919df-PT_4347ZBEX-ATM-chr11:108271506-108273506.bam.bai
45 changes: 37 additions & 8 deletions analyses/01-cram-to-bam.sh → analyses/run-ggsashimi.sh
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Expand Up @@ -5,7 +5,7 @@ kf_id_col=1 # KF patient ID column
chr_col=3 # Chromosome
pos_col=4 # Position
label_col=11 # Additional label to add to plot for identification, i.e. gene
window=10000 # Bases to plot either side of the position given
window=1000 # Bases to plot either side of the position given

## Set up input files
while getopts i:m:k:c:p:l: opt; do
Expand Down Expand Up @@ -49,6 +49,26 @@ else
fi
fi

## Download GENCODE v39 annotations
URL="https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_39/gencode.v39.annotation.gtf.gz"
gencode="../data/gencode.v39.annotation.gtf"

if [ -f "$gencode" ]; then
echo "Using gencode: $gencode"
else
echo "Downloading gencode..."
curl -L -o "$gencode.gz" "$URL"

# Verify download succeeded
if [ $? -eq 0 ]; then
gunzip $gencode.gz
echo "Download complete: $gencode"
else
echo "Download failed."
exit 1
fi
fi

####################################################

# Loop through variant file
Expand All @@ -66,7 +86,8 @@ while read line; do

## get file id
crams=$(grep "$KF_id" $manifest | grep "Aligned.out.sorted.cram" | grep -v "crai" | cut -f2)

input_path="results/${KF_id}-${label}-${coordinates}.tsv"

## loop through each CRAM per patient
## TODO: Make select from BS_ID an option?
for cram in $crams; do
Expand All @@ -76,17 +97,25 @@ while read line; do
prefix=$(basename "$cram" .Aligned.out.sorted.cram)

echo "Converting $cram_path"
bam_path="results/bams/${prefix}-${KF_id}-${label}-${coordinates}.bam"
# input_path="variants/${prefix}-${KF_id}-${label}-${coordinates}.tsv"

bam_path="bams/${prefix}-${KF_id}-${label}-${coordinates}.bam"

samtools view \
-T $ref_genome \
-b \
"$cram_path" \
"$coordinates" \
-o "$bam_path"
-o "results/$bam_path"

samtools index "$bam_path"
samtools index "results/$bam_path"

# create input tsv for ggsashimi
echo "$KF_id"$'\t'"$bam_path"$'\t'"$prefix" >> "$input_path"
done
done < <(tail -n +2 $input_file)

# run ggsashimi
python3 ../ggsashimi.py -b "$input_path" -c "$coordinates" --shrink \
-g $gencode -P input/palette.txt \
-C 1 -O 1 -A median_j -M 3 \
-o "plots/${label}-${KF_id}-${coordinates}"
Comment on lines +116 to +119
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@rjcorb rjcorb Nov 26, 2025

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Can you make some of these parameters command line arguments? I think the --shrink and -M arguments would be useful, and any parameters that control annotation height


done < <(tail -n +2 $input_file)
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