darren/reproduce_setup
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differences to prod server (main) #1

Merged
darren merged 2 commits from pgx-setup into main 2025-08-18 12:46:51 +00:00
Conversation 0 Commits 2 Files Changed 17 +28 -19
17 changed files with 28 additions and 19 deletions
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4
pgx-main/.nextflow/history
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@@ -1,4 +0,0 @@
2025-06-14 14:39:46 6m 40s hopeful_booth OK f9254a4b2675c5f6bb6a9969be9e5b02 bb9b6602-e05a-4409-8d0d-e8f422a1e0a5 nextflow run main.nf -profile standard --build hg38 --gene cyp2d6
2025-08-13 09:58:41 1m 2s high_noether OK f9254a4b2675c5f6bb6a9969be9e5b02 330f6826-005b-4b91-9370-fd093d4a1cfb nextflow run main.nf -profile standard --build hg38 --gene cyp2d6
2025-08-13 10:05:24 2m 25s lethal_euler OK f9254a4b2675c5f6bb6a9969be9e5b02 68e933cc-796e-4b58-9828-6a74d6dd59da nextflow run main.nf -profile standard --build hg38 --gene cyp2d6
2025-08-14 12:43:20 2m 32s mighty_brattain OK f9254a4b2675c5f6bb6a9969be9e5b02 9f6cb1a5-cd74-4ad5-b523-80d635011563 nextflow run main.nf -profile standard --build hg38 --gene cyp2d6

14
pgx-main/README.md
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@@ -12,11 +12,23 @@ git clone https://github.com/SBIMB/StellarPGx.git pgx-main
### Prepare main directory
```bash
cp -r pgx-engine-wrapper/* pgx-main/
mv pgx-main/test3.bed pgx-main/resources/cyp2d6/cyp_hg38/test3.bed
mkdir pgx-main/pgx_results
rm pgx-main/data/*
```
### Update the Chr definitions in main.nf
Update all Chr<#> to just <#> in `main.nf` (e.g. Chr1 should be 1). Important are lines 226-230 in `main.nf` for cyp2d6.
```groovy
if (params.gene=='cyp2d6') {
chrom = "22"
region_a1 = "22:42126000-42137500"
region_a2 = "042126000-042137500"
region_b1 = "22:42126300-42132400"
region_b2 = "042126300-042132400"
transcript = "ENST00000645361"
```
### Place fasta files into pgx-main directory
(`hg38.fa`, `hg38.fa.fai`). For example:
```bash

6
pgx-main/main.bac.nf
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@@ -224,10 +224,10 @@ if (params.build=='b37') {
debug38 = "--minimum_extract_score_over_homref=0"
if (params.gene=='cyp2d6') {
chrom = "22"
region_a1 = "22:42126000-42137500"
chrom = "chr22"
region_a1 = "chr22:42126000-42137500"
region_a2 = "042126000-042137500"
region_b1 = "22:42126300-42132400"
region_b1 = "chr22:42126300-42132400"
region_b2 = "042126300-042132400"
transcript = "ENST00000645361"

3
pgx-main/main.nf
View File

@@ -773,7 +773,7 @@ process call_stars {
publishDir "$output_folder/$gene_name/alleles", mode: 'copy', overwrite: 'true'
//errorStrategy 'ignore'
errorStrategy 'ignore'
tag "${name}"
input:
@@ -788,6 +788,7 @@ process call_stars {
"""
python3 ${caller_dir}/stellarpgx.py ${db}/diplo_db_debugged2.dbs ${name}_vars/${name}_core_snvs.dip ${name}_vars/${name}_full.dip ${name}_vars/${name}_gt.dip ${db}/genotypes4.dbs ${name}_gene_del/${name}_gene_del_summary.txt ${name}_gene_dup/${name}_gene_dup_summary.txt ${name}_${gene_name}_dp ${db}/haps_var_new.dbs ${db}/a_scores.dbs > ${name}_${gene_name}.alleles
"""
}

10
pgx-main/pgx_diplotypes_rsids.tsv
View File

@@ -1,6 +1,6 @@
ABCG2 CFTR CYP2B6 CYP2C19 CYP2C8 CYP2C9 CYP2D6 CYP3A4 CYP3A5 DPYD HLA-A HLA-B IFNL3 NAT2 NUDT15 RYR1 SLCO1B1 TPMT UGT1A1 VKORC1 rsids (no phenotype) rsids (all) rsids (fulgent/no phenotype) rsids (fulgent/all)
CAN-NA12003-29Mar2025_S25_pgx_result rs2231142 reference (G)/rs2231142 reference (G) ivacaftor non-responsive CFTR sequence/ivacaftor non-responsive CFTR sequence *6/*6 *1/*1 *1/*2 *35/*4 *1/*1 *1/*3 Reference/Reference reference/reference reference/reference rs12979860 reference (C)/rs12979860 reference (C) *5D/*5D *1/*1 Reference/Reference *1/*5 *1/*1 *1/*80 rs9923231 variant (T)/rs9923231 variant (T) rs1045642 AG, rs10509681 CT, rs1057910 AA, rs11045819 CC, rs115232898 TT, rs11572080 CC, rs11572103 TT, rs12248560 CC, rs12777823 GG, rs148994843 CC, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1799853 CT, rs1801133 AA, rs1801160 CC, rs1801266 GG, rs1801268 CC, rs2032582 AC, rs2108622 CC, rs2231142 GG, rs2279343 GG, rs2306283 AA, rs2740574 CT, rs3093105 AA, rs3211371 CC, rs35599367 GG, rs3745274 TT, rs3892097 CT, rs4149056 CT, rs4341 CG, rs4343 AG, rs4680 AG, rs56005131 GG, rs59086055 GG, rs72549306 CC, rs75017182 GG, rs776746 CT, rs78060119 CC, rs8192709 CC, rs9923231 TT rs1045642 AG, rs10509681 CT, rs1057910 AA, rs11045819 CC, rs115232898 TT, rs11572080 CC, rs11572103 TT, rs12248560 CC, rs12777823 GG, rs148994843 CC, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1799853 CT, rs1801133 AA, rs1801160 CC, rs1801266 GG, rs1801268 CC, rs2032582 AC, rs2108622 CC, rs2231142 GG, rs2279343 GG, rs2306283 AA, rs2740574 CT, rs3093105 AA, rs3211371 CC, rs35599367 GG, rs3745274 TT, rs3892097 CT, rs4149056 CT, rs4341 CG, rs4343 AG, rs4680 AG, rs56005131 GG, rs59086055 GG, rs72549306 CC, rs75017182 GG, rs776746 CT, rs78060119 CC, rs8192709 CC, rs9923231 TT rs1045642 AG, rs10509681 CT, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1801133 AA, rs2032582 AC, rs2108622 CC, rs2740574 CT, rs4149056 CT, rs4343 AG, rs4680 AG, rs9923231 TT rs1045642 AG, rs10509681 CT, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1801133 AA, rs2032582 AC, rs2108622 CC, rs2740574 CT, rs4149056 CT, rs4343 AG, rs4680 AG, rs9923231 TT
CAN-NA12878-1-29Mar2025_S20_pgx_result rs2231142 reference (G)/rs2231142 reference (G) ivacaftor non-responsive CFTR sequence/ivacaftor non-responsive CFTR sequence *1/*1 *1/*2 *1/*2 *1/*10 *1/*1 *3/*3 Reference/Reference reference/reference reference/reference rs12979860 reference (C)/rs12979860 variant (T) *4/*5D *1/*1 Reference/Reference *1/*5 *1/*1 *1/*80 rs9923231 reference (C)/rs9923231 variant (T) rs1045642 AG, rs10509681 CT, rs1057910 AA, rs11045819 CC, rs115232898 TT, rs11572080 CC, rs11572103 TT, rs12248560 CC, rs12777823 AG, rs148994843 CC, rs1695 AG, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC, rs1799853 CT, rs1801133 AG, rs1801160 CC, rs1801266 GG, rs1801268 CC, rs2032582 CC, rs2108622 CC, rs2231142 GG, rs2279343 AA, rs2306283 AA, rs2740574 TT, rs3093105 AA, rs3211371 CC, rs35599367 GG, rs3745274 GG, rs3892097 CT, rs4149056 CT, rs4341 CC, rs4343 AA, rs4680 AG, rs56005131 GG, rs59086055 GG, rs72549306 CC, rs75017182 GG, rs776746 CC, rs78060119 CC, rs8192709 CC, rs9923231 CT rs1045642 AG, rs10509681 CT, rs1057910 AA, rs11045819 CC, rs115232898 TT, rs11572080 CC, rs11572103 TT, rs12248560 CC, rs12777823 AG, rs148994843 CC, rs1695 AG, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC, rs1799853 CT, rs1801133 AG, rs1801160 CC, rs1801266 GG, rs1801268 CC, rs2032582 CC, rs2108622 CC, rs2231142 GG, rs2279343 AA, rs2306283 AA, rs2740574 TT, rs3093105 AA, rs3211371 CC, rs35599367 GG, rs3745274 GG, rs3892097 CT, rs4149056 CT, rs4341 CC, rs4343 AA, rs4680 AG, rs56005131 GG, rs59086055 GG, rs72549306 CC, rs75017182 GG, rs776746 CC, rs78060119 CC, rs8192709 CC, rs9923231 CT rs1045642 AG, rs10509681 CT, rs1695 AG, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC, rs1801133 AG, rs2032582 CC, rs2108622 CC, rs2740574 TT, rs4149056 CT, rs4343 AA, rs4680 AG, rs9923231 CT rs1045642 AG, rs10509681 CT, rs1695 AG, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC, rs1801133 AG, rs2032582 CC, rs2108622 CC, rs2740574 TT, rs4149056 CT, rs4343 AA, rs4680 AG, rs9923231 CT
CAN-NA19226-29Mar2025_S29_pgx_result rs2231142 reference (G)/rs2231142 reference (G) ivacaftor non-responsive CFTR sequence/ivacaftor non-responsive CFTR sequence *1/*18 *1/*2 *1.001/*1.001 *1/*8 *2/*2x2 *1/*1 *1/*6 Reference/Reference reference/reference reference/reference rs12979860 reference (C)/rs12979860 variant (T) *4/*5D *1/*1 Reference/Reference *1/*1 *1/*1 *1/*1 rs9923231 reference (C)/rs9923231 reference (C) rs1045642 AG, rs10509681 TT, rs1057910 AA, rs11045819 CC, rs115232898 TT, rs11572080 CC, rs11572103 TT, rs12248560 CC, rs12777823 AA, rs148994843 CC, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1799853 CC, rs1799978 CT, rs1801160 CC, rs1801266 GG, rs1801268 CC, rs2032582 CC, rs2108622 CC, rs2231142 GG, rs2279343 AG, rs2306283 AA, rs2740574 CC, rs3093105 AC, rs3211371 CC, rs35599367 GG, rs3745274 GT, rs3892097 CC, rs4149056 TT, rs4343 AG, rs4680 AA, rs56005131 GG, rs59086055 GG, rs72549306 CC, rs75017182 GG, rs776746 TT, rs78060119 CC, rs8192709 CC, rs9923231 CC rs1045642 AG, rs10509681 TT, rs1057910 AA, rs11045819 CC, rs115232898 TT, rs11572080 CC, rs11572103 TT, rs12248560 CC, rs12777823 AA, rs148994843 CC, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1799853 CC, rs1799978 CT, rs1801160 CC, rs1801266 GG, rs1801268 CC, rs2032582 CC, rs2108622 CC, rs2231142 GG, rs2279343 AG, rs2306283 AA, rs2740574 CC, rs3093105 AC, rs3211371 CC, rs35599367 GG, rs3745274 GT, rs3892097 CC, rs4149056 TT, rs4343 AG, rs4680 AA, rs56005131 GG, rs59086055 GG, rs72549306 CC, rs75017182 GG, rs776746 TT, rs78060119 CC, rs8192709 CC, rs9923231 CC rs1045642 AG, rs10509681 TT, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1799978 CT, rs2032582 CC, rs2108622 CC, rs2740574 CC, rs4149056 TT, rs4343 AG, rs4680 AA, rs9923231 CC rs1045642 AG, rs10509681 TT, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1799978 CT, rs2032582 CC, rs2108622 CC, rs2740574 CC, rs4149056 TT, rs4343 AG, rs4680 AA, rs9923231 CC
CAN-NA19239-29Mar2025_S32_pgx_result rs2231142 reference (G)/rs2231142 reference (G) ivacaftor non-responsive CFTR sequence/ivacaftor non-responsive CFTR sequence *1/*6 *17/*38 *1.001/*1.001 *1/*1 *15/*17 *1/*1 *1/*1 Reference/Reference reference/reference reference/reference rs12979860 reference (C)/rs12979860 variant (T) *14/*4 *1/*1 Reference/Reference *1/*1 *1/*1 *80/*80 rs9923231 reference (C)/rs9923231 reference (C) rs1045642 GG, rs10509681 TT, rs1057910 AA, rs11045819 CC, rs115232898 TT, rs11572080 CC, rs11572103 TT, rs12248560 CT, rs12777823 GG, rs148994843 CC, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1799853 CC, rs1799978 CT, rs1801160 CC, rs1801266 GG, rs1801268 CC, rs2032582 CC, rs2108622 CC, rs2231142 GG, rs2279343 AG, rs2306283 AA, rs2740574 CT, rs3093105 AA, rs3211371 CC, rs35599367 GG, rs3745274 GT, rs3892097 CC, rs4149056 TT, rs4343 AG, rs4680 AG, rs56005131 GG, rs59086055 GG, rs7200749 AG, rs72549306 CC, rs75017182 GG, rs776746 TT, rs78060119 CC, rs8192709 CC, rs9923231 CC rs1045642 GG, rs10509681 TT, rs1057910 AA, rs11045819 CC, rs115232898 TT, rs11572080 CC, rs11572103 TT, rs12248560 CT, rs12777823 GG, rs148994843 CC, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1799853 CC, rs1799978 CT, rs1801160 CC, rs1801266 GG, rs1801268 CC, rs2032582 CC, rs2108622 CC, rs2231142 GG, rs2279343 AG, rs2306283 AA, rs2740574 CT, rs3093105 AA, rs3211371 CC, rs35599367 GG, rs3745274 GT, rs3892097 CC, rs4149056 TT, rs4343 AG, rs4680 AG, rs56005131 GG, rs59086055 GG, rs7200749 AG, rs72549306 CC, rs75017182 GG, rs776746 TT, rs78060119 CC, rs8192709 CC, rs9923231 CC rs1045642 GG, rs10509681 TT, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1799978 CT, rs2032582 CC, rs2108622 CC, rs2740574 CT, rs4149056 TT, rs4343 AG, rs4680 AG, rs9923231 CC rs1045642 GG, rs10509681 TT, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1799978 CT, rs2032582 CC, rs2108622 CC, rs2740574 CT, rs4149056 TT, rs4343 AG, rs4680 AG, rs9923231 CC
CAN-NA24385-2-29Mar2025_S23_pgx_result rs2231142 reference (G)/rs2231142 reference (G) ivacaftor non-responsive CFTR sequence/ivacaftor non-responsive CFTR sequence *1/*5 *1/*1 *1.001/*1.001 *1/*1 *2/*4 *1/*1 *3/*3 Reference/Reference reference/reference reference/reference rs12979860 reference (C)/rs12979860 reference (C) *4/*6B *1/*1 Reference/Reference *1/*1 *1/*1 *1/*1 rs9923231 variant (T)/rs9923231 variant (T) rs1045642 GG, rs10509681 TT, rs1057910 AA, rs11045819 CC, rs115232898 TT, rs11572080 CC, rs11572103 TT, rs12248560 CC, rs12777823 GG, rs148994843 CC, rs1799853 CC, rs1801133 AG, rs1801160 CC, rs1801266 GG, rs1801268 CC, rs2032582 CC, rs2108622 CT, rs2231142 GG, rs2279343 AA, rs2306283 AA, rs2740574 TT, rs3093105 AC, rs3211371 CT, rs35599367 GG, rs3745274 GG, rs3892097 CT, rs4149056 TT, rs4680 AA, rs56005131 GG, rs59086055 GG, rs72549306 CC, rs75017182 GG, rs776746 CC, rs78060119 CC, rs8192709 CC, rs9923231 TT rs1045642 GG, rs10509681 TT, rs1057910 AA, rs11045819 CC, rs115232898 TT, rs11572080 CC, rs11572103 TT, rs12248560 CC, rs12777823 GG, rs148994843 CC, rs1799853 CC, rs1801133 AG, rs1801160 CC, rs1801266 GG, rs1801268 CC, rs2032582 CC, rs2108622 CT, rs2231142 GG, rs2279343 AA, rs2306283 AA, rs2740574 TT, rs3093105 AC, rs3211371 CT, rs35599367 GG, rs3745274 GG, rs3892097 CT, rs4149056 TT, rs4680 AA, rs56005131 GG, rs59086055 GG, rs72549306 CC, rs75017182 GG, rs776746 CC, rs78060119 CC, rs8192709 CC, rs9923231 TT rs1045642 GG, rs10509681 TT, rs1801133 AG, rs2032582 CC, rs2108622 CT, rs2740574 TT, rs4149056 TT, rs4680 AA, rs9923231 TT rs1045642 GG, rs10509681 TT, rs1801133 AG, rs2032582 CC, rs2108622 CT, rs2740574 TT, rs4149056 TT, rs4680 AA, rs9923231 TT
CAN-NA12003-29Mar2025_S25_pgx_result rs2231142 reference (G)/rs2231142 reference (G) ivacaftor non-responsive CFTR sequence/ivacaftor non-responsive CFTR sequence *6/*6 *1/*1 *1/*2 *1/*1 *1/*1 *1/*3 Reference/Reference reference/reference reference/reference rs12979860 reference (C)/rs12979860 reference (C) *5D/*5D *1/*1 Reference/Reference *1/*5 *1/*1 *1/*80 rs9923231 variant (T)/rs9923231 variant (T) rs1045642 AG, rs10509681 CT, rs1057910 AA, rs11045819 CC, rs115232898 TT, rs11572080 CC, rs11572103 TT, rs12248560 CC, rs12777823 GG, rs148994843 CC, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1799853 CT, rs1801133 AA, rs1801160 CC, rs1801266 GG, rs1801268 CC, rs2032582 AC, rs2108622 CC, rs2231142 GG, rs2279343 GG, rs2306283 AA, rs2740574 CT, rs3093105 AA, rs3211371 CC, rs35599367 GG, rs3745274 TT, rs3892097 CT, rs4149056 CT, rs4341 CG, rs4343 AG, rs4680 AG, rs56005131 GG, rs59086055 GG, rs72549306 CC, rs75017182 GG, rs776746 CT, rs78060119 CC, rs8192709 CC, rs9923231 TT rs1045642 AG, rs10509681 CT, rs1057910 AA, rs11045819 CC, rs115232898 TT, rs11572080 CC, rs11572103 TT, rs12248560 CC, rs12777823 GG, rs148994843 CC, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1799853 CT, rs1801133 AA, rs1801160 CC, rs1801266 GG, rs1801268 CC, rs2032582 AC, rs2108622 CC, rs2231142 GG, rs2279343 GG, rs2306283 AA, rs2740574 CT, rs3093105 AA, rs3211371 CC, rs35599367 GG, rs3745274 TT, rs3892097 CT, rs4149056 CT, rs4341 CG, rs4343 AG, rs4680 AG, rs56005131 GG, rs59086055 GG, rs72549306 CC, rs75017182 GG, rs776746 CT, rs78060119 CC, rs8192709 CC, rs9923231 TT rs1045642 AG, rs10509681 CT, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1801133 AA, rs2032582 AC, rs2108622 CC, rs2740574 CT, rs4149056 CT, rs4343 AG, rs4680 AG, rs9923231 TT rs1045642 AG, rs10509681 CT, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1801133 AA, rs2032582 AC, rs2108622 CC, rs2740574 CT, rs4149056 CT, rs4343 AG, rs4680 AG, rs9923231 TT
CAN-NA12878-1-29Mar2025_S20_pgx_result rs2231142 reference (G)/rs2231142 reference (G) ivacaftor non-responsive CFTR sequence/ivacaftor non-responsive CFTR sequence *1/*1 *1/*2 *1/*2 *1/*1x2 *1/*1 *3/*3 Reference/Reference reference/reference reference/reference rs12979860 reference (C)/rs12979860 variant (T) *4/*5D *1/*1 Reference/Reference *1/*5 *1/*1 *1/*80 rs9923231 reference (C)/rs9923231 variant (T) rs1045642 AG, rs10509681 CT, rs1057910 AA, rs11045819 CC, rs115232898 TT, rs11572080 CC, rs11572103 TT, rs12248560 CC, rs12777823 AG, rs148994843 CC, rs1695 AG, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC, rs1799853 CT, rs1801133 AG, rs1801160 CC, rs1801266 GG, rs1801268 CC, rs2032582 CC, rs2108622 CC, rs2231142 GG, rs2279343 AA, rs2306283 AA, rs2740574 TT, rs3093105 AA, rs3211371 CC, rs35599367 GG, rs3745274 GG, rs3892097 CT, rs4149056 CT, rs4341 CC, rs4343 AA, rs4680 AG, rs56005131 GG, rs59086055 GG, rs72549306 CC, rs75017182 GG, rs776746 CC, rs78060119 CC, rs8192709 CC, rs9923231 CT rs1045642 AG, rs10509681 CT, rs1057910 AA, rs11045819 CC, rs115232898 TT, rs11572080 CC, rs11572103 TT, rs12248560 CC, rs12777823 AG, rs148994843 CC, rs1695 AG, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC, rs1799853 CT, rs1801133 AG, rs1801160 CC, rs1801266 GG, rs1801268 CC, rs2032582 CC, rs2108622 CC, rs2231142 GG, rs2279343 AA, rs2306283 AA, rs2740574 TT, rs3093105 AA, rs3211371 CC, rs35599367 GG, rs3745274 GG, rs3892097 CT, rs4149056 CT, rs4341 CC, rs4343 AA, rs4680 AG, rs56005131 GG, rs59086055 GG, rs72549306 CC, rs75017182 GG, rs776746 CC, rs78060119 CC, rs8192709 CC, rs9923231 CT rs1045642 AG, rs10509681 CT, rs1695 AG, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC, rs1801133 AG, rs2032582 CC, rs2108622 CC, rs2740574 TT, rs4149056 CT, rs4343 AA, rs4680 AG, rs9923231 CT rs1045642 AG, rs10509681 CT, rs1695 AG, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC, rs1801133 AG, rs2032582 CC, rs2108622 CC, rs2740574 TT, rs4149056 CT, rs4343 AA, rs4680 AG, rs9923231 CT
CAN-NA19226-29Mar2025_S29_pgx_result rs2231142 reference (G)/rs2231142 reference (G) ivacaftor non-responsive CFTR sequence/ivacaftor non-responsive CFTR sequence *1/*18 *1/*2 *1.001/*1.001 *1/*8 *1/*1x2 *1/*1 *1/*6 Reference/Reference reference/reference reference/reference rs12979860 reference (C)/rs12979860 variant (T) *4/*5D *1/*1 Reference/Reference *1/*1 *1/*1 *1/*1 rs9923231 reference (C)/rs9923231 reference (C) rs1045642 AG, rs10509681 TT, rs1057910 AA, rs11045819 CC, rs115232898 TT, rs11572080 CC, rs11572103 TT, rs12248560 CC, rs12777823 AA, rs148994843 CC, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1799853 CC, rs1799978 CT, rs1801160 CC, rs1801266 GG, rs1801268 CC, rs2032582 CC, rs2108622 CC, rs2231142 GG, rs2279343 AG, rs2306283 AA, rs2740574 CC, rs3093105 AC, rs3211371 CC, rs35599367 GG, rs3745274 GT, rs3892097 CC, rs4149056 TT, rs4343 AG, rs4680 AA, rs56005131 GG, rs59086055 GG, rs72549306 CC, rs75017182 GG, rs776746 TT, rs78060119 CC, rs8192709 CC, rs9923231 CC rs1045642 AG, rs10509681 TT, rs1057910 AA, rs11045819 CC, rs115232898 TT, rs11572080 CC, rs11572103 TT, rs12248560 CC, rs12777823 AA, rs148994843 CC, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1799853 CC, rs1799978 CT, rs1801160 CC, rs1801266 GG, rs1801268 CC, rs2032582 CC, rs2108622 CC, rs2231142 GG, rs2279343 AG, rs2306283 AA, rs2740574 CC, rs3093105 AC, rs3211371 CC, rs35599367 GG, rs3745274 GT, rs3892097 CC, rs4149056 TT, rs4343 AG, rs4680 AA, rs56005131 GG, rs59086055 GG, rs72549306 CC, rs75017182 GG, rs776746 TT, rs78060119 CC, rs8192709 CC, rs9923231 CC rs1045642 AG, rs10509681 TT, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1799978 CT, rs2032582 CC, rs2108622 CC, rs2740574 CC, rs4149056 TT, rs4343 AG, rs4680 AA, rs9923231 CC rs1045642 AG, rs10509681 TT, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1799978 CT, rs2032582 CC, rs2108622 CC, rs2740574 CC, rs4149056 TT, rs4343 AG, rs4680 AA, rs9923231 CC
CAN-NA19239-29Mar2025_S32_pgx_result rs2231142 reference (G)/rs2231142 reference (G) ivacaftor non-responsive CFTR sequence/ivacaftor non-responsive CFTR sequence *1/*6 *17/*38 *1.001/*1.001 *1/*1 *1/*1 *1/*1 *1/*1 Reference/Reference reference/reference reference/reference rs12979860 reference (C)/rs12979860 variant (T) *14/*4 *1/*1 Reference/Reference *1/*1 *1/*1 *80/*80 rs9923231 reference (C)/rs9923231 reference (C) rs1045642 GG, rs10509681 TT, rs1057910 AA, rs11045819 CC, rs115232898 TT, rs11572080 CC, rs11572103 TT, rs12248560 CT, rs12777823 GG, rs148994843 CC, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1799853 CC, rs1799978 CT, rs1801160 CC, rs1801266 GG, rs1801268 CC, rs2032582 CC, rs2108622 CC, rs2231142 GG, rs2279343 AG, rs2306283 AA, rs2740574 CT, rs3093105 AA, rs3211371 CC, rs35599367 GG, rs3745274 GT, rs3892097 CC, rs4149056 TT, rs4343 AG, rs4680 AG, rs56005131 GG, rs59086055 GG, rs7200749 AG, rs72549306 CC, rs75017182 GG, rs776746 TT, rs78060119 CC, rs8192709 CC, rs9923231 CC rs1045642 GG, rs10509681 TT, rs1057910 AA, rs11045819 CC, rs115232898 TT, rs11572080 CC, rs11572103 TT, rs12248560 CT, rs12777823 GG, rs148994843 CC, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1799853 CC, rs1799978 CT, rs1801160 CC, rs1801266 GG, rs1801268 CC, rs2032582 CC, rs2108622 CC, rs2231142 GG, rs2279343 AG, rs2306283 AA, rs2740574 CT, rs3093105 AA, rs3211371 CC, rs35599367 GG, rs3745274 GT, rs3892097 CC, rs4149056 TT, rs4343 AG, rs4680 AG, rs56005131 GG, rs59086055 GG, rs7200749 AG, rs72549306 CC, rs75017182 GG, rs776746 TT, rs78060119 CC, rs8192709 CC, rs9923231 CC rs1045642 GG, rs10509681 TT, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1799978 CT, rs2032582 CC, rs2108622 CC, rs2740574 CT, rs4149056 TT, rs4343 AG, rs4680 AG, rs9923231 CC rs1045642 GG, rs10509681 TT, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1799978 CT, rs2032582 CC, rs2108622 CC, rs2740574 CT, rs4149056 TT, rs4343 AG, rs4680 AG, rs9923231 CC
CAN-NA24385-2-29Mar2025_S23_pgx_result rs2231142 reference (G)/rs2231142 reference (G) ivacaftor non-responsive CFTR sequence/ivacaftor non-responsive CFTR sequence *1/*5 *1/*1 *1.001/*1.001 *1/*1 *1/*1 *1/*1 *3/*3 Reference/Reference reference/reference reference/reference rs12979860 reference (C)/rs12979860 reference (C) *4/*6B *1/*1 Reference/Reference *1/*1 *1/*1 *1/*1 rs9923231 variant (T)/rs9923231 variant (T) rs1045642 GG, rs10509681 TT, rs1057910 AA, rs11045819 CC, rs115232898 TT, rs11572080 CC, rs11572103 TT, rs12248560 CC, rs12777823 GG, rs148994843 CC, rs1799853 CC, rs1801133 AG, rs1801160 CC, rs1801266 GG, rs1801268 CC, rs2032582 CC, rs2108622 CT, rs2231142 GG, rs2279343 AA, rs2306283 AA, rs2740574 TT, rs3093105 AC, rs3211371 CT, rs35599367 GG, rs3745274 GG, rs3892097 CT, rs4149056 TT, rs4680 AA, rs56005131 GG, rs59086055 GG, rs72549306 CC, rs75017182 GG, rs776746 CC, rs78060119 CC, rs8192709 CC, rs9923231 TT rs1045642 GG, rs10509681 TT, rs1057910 AA, rs11045819 CC, rs115232898 TT, rs11572080 CC, rs11572103 TT, rs12248560 CC, rs12777823 GG, rs148994843 CC, rs1799853 CC, rs1801133 AG, rs1801160 CC, rs1801266 GG, rs1801268 CC, rs2032582 CC, rs2108622 CT, rs2231142 GG, rs2279343 AA, rs2306283 AA, rs2740574 TT, rs3093105 AC, rs3211371 CT, rs35599367 GG, rs3745274 GG, rs3892097 CT, rs4149056 TT, rs4680 AA, rs56005131 GG, rs59086055 GG, rs72549306 CC, rs75017182 GG, rs776746 CC, rs78060119 CC, rs8192709 CC, rs9923231 TT rs1045642 GG, rs10509681 TT, rs1801133 AG, rs2032582 CC, rs2108622 CT, rs2740574 TT, rs4149056 TT, rs4680 AA, rs9923231 TT rs1045642 GG, rs10509681 TT, rs1801133 AG, rs2032582 CC, rs2108622 CT, rs2740574 TT, rs4149056 TT, rs4680 AA, rs9923231 TT
1 ABCG2 CFTR CYP2B6 CYP2C19 CYP2C8 CYP2C9 CYP2D6 CYP3A4 CYP3A5 DPYD HLA-A HLA-B IFNL3 NAT2 NUDT15 RYR1 SLCO1B1 TPMT UGT1A1 VKORC1 rsids (no phenotype) rsids (all) rsids (fulgent/no phenotype) rsids (fulgent/all)
2 CAN-NA12003-29Mar2025_S25_pgx_result rs2231142 reference (G)/rs2231142 reference (G) ivacaftor non-responsive CFTR sequence/ivacaftor non-responsive CFTR sequence *6/*6 *1/*1 *1/*2 *35/*4 *1/*1 *1/*1 *1/*3 Reference/Reference reference/reference reference/reference rs12979860 reference (C)/rs12979860 reference (C) *5D/*5D *1/*1 Reference/Reference *1/*5 *1/*1 *1/*80 rs9923231 variant (T)/rs9923231 variant (T) rs1045642 AG, rs10509681 CT, rs1057910 AA, rs11045819 CC, rs115232898 TT, rs11572080 CC, rs11572103 TT, rs12248560 CC, rs12777823 GG, rs148994843 CC, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1799853 CT, rs1801133 AA, rs1801160 CC, rs1801266 GG, rs1801268 CC, rs2032582 AC, rs2108622 CC, rs2231142 GG, rs2279343 GG, rs2306283 AA, rs2740574 CT, rs3093105 AA, rs3211371 CC, rs35599367 GG, rs3745274 TT, rs3892097 CT, rs4149056 CT, rs4341 CG, rs4343 AG, rs4680 AG, rs56005131 GG, rs59086055 GG, rs72549306 CC, rs75017182 GG, rs776746 CT, rs78060119 CC, rs8192709 CC, rs9923231 TT rs1045642 AG, rs10509681 CT, rs1057910 AA, rs11045819 CC, rs115232898 TT, rs11572080 CC, rs11572103 TT, rs12248560 CC, rs12777823 GG, rs148994843 CC, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1799853 CT, rs1801133 AA, rs1801160 CC, rs1801266 GG, rs1801268 CC, rs2032582 AC, rs2108622 CC, rs2231142 GG, rs2279343 GG, rs2306283 AA, rs2740574 CT, rs3093105 AA, rs3211371 CC, rs35599367 GG, rs3745274 TT, rs3892097 CT, rs4149056 CT, rs4341 CG, rs4343 AG, rs4680 AG, rs56005131 GG, rs59086055 GG, rs72549306 CC, rs75017182 GG, rs776746 CT, rs78060119 CC, rs8192709 CC, rs9923231 TT rs1045642 AG, rs10509681 CT, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1801133 AA, rs2032582 AC, rs2108622 CC, rs2740574 CT, rs4149056 CT, rs4343 AG, rs4680 AG, rs9923231 TT rs1045642 AG, rs10509681 CT, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1801133 AA, rs2032582 AC, rs2108622 CC, rs2740574 CT, rs4149056 CT, rs4343 AG, rs4680 AG, rs9923231 TT
3 CAN-NA12878-1-29Mar2025_S20_pgx_result rs2231142 reference (G)/rs2231142 reference (G) ivacaftor non-responsive CFTR sequence/ivacaftor non-responsive CFTR sequence *1/*1 *1/*2 *1/*2 *1/*10 *1/*1x2 *1/*1 *3/*3 Reference/Reference reference/reference reference/reference rs12979860 reference (C)/rs12979860 variant (T) *4/*5D *1/*1 Reference/Reference *1/*5 *1/*1 *1/*80 rs9923231 reference (C)/rs9923231 variant (T) rs1045642 AG, rs10509681 CT, rs1057910 AA, rs11045819 CC, rs115232898 TT, rs11572080 CC, rs11572103 TT, rs12248560 CC, rs12777823 AG, rs148994843 CC, rs1695 AG, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC, rs1799853 CT, rs1801133 AG, rs1801160 CC, rs1801266 GG, rs1801268 CC, rs2032582 CC, rs2108622 CC, rs2231142 GG, rs2279343 AA, rs2306283 AA, rs2740574 TT, rs3093105 AA, rs3211371 CC, rs35599367 GG, rs3745274 GG, rs3892097 CT, rs4149056 CT, rs4341 CC, rs4343 AA, rs4680 AG, rs56005131 GG, rs59086055 GG, rs72549306 CC, rs75017182 GG, rs776746 CC, rs78060119 CC, rs8192709 CC, rs9923231 CT rs1045642 AG, rs10509681 CT, rs1057910 AA, rs11045819 CC, rs115232898 TT, rs11572080 CC, rs11572103 TT, rs12248560 CC, rs12777823 AG, rs148994843 CC, rs1695 AG, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC, rs1799853 CT, rs1801133 AG, rs1801160 CC, rs1801266 GG, rs1801268 CC, rs2032582 CC, rs2108622 CC, rs2231142 GG, rs2279343 AA, rs2306283 AA, rs2740574 TT, rs3093105 AA, rs3211371 CC, rs35599367 GG, rs3745274 GG, rs3892097 CT, rs4149056 CT, rs4341 CC, rs4343 AA, rs4680 AG, rs56005131 GG, rs59086055 GG, rs72549306 CC, rs75017182 GG, rs776746 CC, rs78060119 CC, rs8192709 CC, rs9923231 CT rs1045642 AG, rs10509681 CT, rs1695 AG, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC, rs1801133 AG, rs2032582 CC, rs2108622 CC, rs2740574 TT, rs4149056 CT, rs4343 AA, rs4680 AG, rs9923231 CT rs1045642 AG, rs10509681 CT, rs1695 AG, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC, rs1801133 AG, rs2032582 CC, rs2108622 CC, rs2740574 TT, rs4149056 CT, rs4343 AA, rs4680 AG, rs9923231 CT
4 CAN-NA19226-29Mar2025_S29_pgx_result rs2231142 reference (G)/rs2231142 reference (G) ivacaftor non-responsive CFTR sequence/ivacaftor non-responsive CFTR sequence *1/*18 *1/*2 *1.001/*1.001 *1/*8 *2/*2x2 *1/*1x2 *1/*1 *1/*6 Reference/Reference reference/reference reference/reference rs12979860 reference (C)/rs12979860 variant (T) *4/*5D *1/*1 Reference/Reference *1/*1 *1/*1 *1/*1 rs9923231 reference (C)/rs9923231 reference (C) rs1045642 AG, rs10509681 TT, rs1057910 AA, rs11045819 CC, rs115232898 TT, rs11572080 CC, rs11572103 TT, rs12248560 CC, rs12777823 AA, rs148994843 CC, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1799853 CC, rs1799978 CT, rs1801160 CC, rs1801266 GG, rs1801268 CC, rs2032582 CC, rs2108622 CC, rs2231142 GG, rs2279343 AG, rs2306283 AA, rs2740574 CC, rs3093105 AC, rs3211371 CC, rs35599367 GG, rs3745274 GT, rs3892097 CC, rs4149056 TT, rs4343 AG, rs4680 AA, rs56005131 GG, rs59086055 GG, rs72549306 CC, rs75017182 GG, rs776746 TT, rs78060119 CC, rs8192709 CC, rs9923231 CC rs1045642 AG, rs10509681 TT, rs1057910 AA, rs11045819 CC, rs115232898 TT, rs11572080 CC, rs11572103 TT, rs12248560 CC, rs12777823 AA, rs148994843 CC, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1799853 CC, rs1799978 CT, rs1801160 CC, rs1801266 GG, rs1801268 CC, rs2032582 CC, rs2108622 CC, rs2231142 GG, rs2279343 AG, rs2306283 AA, rs2740574 CC, rs3093105 AC, rs3211371 CC, rs35599367 GG, rs3745274 GT, rs3892097 CC, rs4149056 TT, rs4343 AG, rs4680 AA, rs56005131 GG, rs59086055 GG, rs72549306 CC, rs75017182 GG, rs776746 TT, rs78060119 CC, rs8192709 CC, rs9923231 CC rs1045642 AG, rs10509681 TT, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1799978 CT, rs2032582 CC, rs2108622 CC, rs2740574 CC, rs4149056 TT, rs4343 AG, rs4680 AA, rs9923231 CC rs1045642 AG, rs10509681 TT, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1799978 CT, rs2032582 CC, rs2108622 CC, rs2740574 CC, rs4149056 TT, rs4343 AG, rs4680 AA, rs9923231 CC
5 CAN-NA19239-29Mar2025_S32_pgx_result rs2231142 reference (G)/rs2231142 reference (G) ivacaftor non-responsive CFTR sequence/ivacaftor non-responsive CFTR sequence *1/*6 *17/*38 *1.001/*1.001 *1/*1 *15/*17 *1/*1 *1/*1 *1/*1 Reference/Reference reference/reference reference/reference rs12979860 reference (C)/rs12979860 variant (T) *14/*4 *1/*1 Reference/Reference *1/*1 *1/*1 *80/*80 rs9923231 reference (C)/rs9923231 reference (C) rs1045642 GG, rs10509681 TT, rs1057910 AA, rs11045819 CC, rs115232898 TT, rs11572080 CC, rs11572103 TT, rs12248560 CT, rs12777823 GG, rs148994843 CC, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1799853 CC, rs1799978 CT, rs1801160 CC, rs1801266 GG, rs1801268 CC, rs2032582 CC, rs2108622 CC, rs2231142 GG, rs2279343 AG, rs2306283 AA, rs2740574 CT, rs3093105 AA, rs3211371 CC, rs35599367 GG, rs3745274 GT, rs3892097 CC, rs4149056 TT, rs4343 AG, rs4680 AG, rs56005131 GG, rs59086055 GG, rs7200749 AG, rs72549306 CC, rs75017182 GG, rs776746 TT, rs78060119 CC, rs8192709 CC, rs9923231 CC rs1045642 GG, rs10509681 TT, rs1057910 AA, rs11045819 CC, rs115232898 TT, rs11572080 CC, rs11572103 TT, rs12248560 CT, rs12777823 GG, rs148994843 CC, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1799853 CC, rs1799978 CT, rs1801160 CC, rs1801266 GG, rs1801268 CC, rs2032582 CC, rs2108622 CC, rs2231142 GG, rs2279343 AG, rs2306283 AA, rs2740574 CT, rs3093105 AA, rs3211371 CC, rs35599367 GG, rs3745274 GT, rs3892097 CC, rs4149056 TT, rs4343 AG, rs4680 AG, rs56005131 GG, rs59086055 GG, rs7200749 AG, rs72549306 CC, rs75017182 GG, rs776746 TT, rs78060119 CC, rs8192709 CC, rs9923231 CC rs1045642 GG, rs10509681 TT, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1799978 CT, rs2032582 CC, rs2108622 CC, rs2740574 CT, rs4149056 TT, rs4343 AG, rs4680 AG, rs9923231 CC rs1045642 GG, rs10509681 TT, rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del, rs1799978 CT, rs2032582 CC, rs2108622 CC, rs2740574 CT, rs4149056 TT, rs4343 AG, rs4680 AG, rs9923231 CC
6 CAN-NA24385-2-29Mar2025_S23_pgx_result rs2231142 reference (G)/rs2231142 reference (G) ivacaftor non-responsive CFTR sequence/ivacaftor non-responsive CFTR sequence *1/*5 *1/*1 *1.001/*1.001 *1/*1 *2/*4 *1/*1 *1/*1 *3/*3 Reference/Reference reference/reference reference/reference rs12979860 reference (C)/rs12979860 reference (C) *4/*6B *1/*1 Reference/Reference *1/*1 *1/*1 *1/*1 rs9923231 variant (T)/rs9923231 variant (T) rs1045642 GG, rs10509681 TT, rs1057910 AA, rs11045819 CC, rs115232898 TT, rs11572080 CC, rs11572103 TT, rs12248560 CC, rs12777823 GG, rs148994843 CC, rs1799853 CC, rs1801133 AG, rs1801160 CC, rs1801266 GG, rs1801268 CC, rs2032582 CC, rs2108622 CT, rs2231142 GG, rs2279343 AA, rs2306283 AA, rs2740574 TT, rs3093105 AC, rs3211371 CT, rs35599367 GG, rs3745274 GG, rs3892097 CT, rs4149056 TT, rs4680 AA, rs56005131 GG, rs59086055 GG, rs72549306 CC, rs75017182 GG, rs776746 CC, rs78060119 CC, rs8192709 CC, rs9923231 TT rs1045642 GG, rs10509681 TT, rs1057910 AA, rs11045819 CC, rs115232898 TT, rs11572080 CC, rs11572103 TT, rs12248560 CC, rs12777823 GG, rs148994843 CC, rs1799853 CC, rs1801133 AG, rs1801160 CC, rs1801266 GG, rs1801268 CC, rs2032582 CC, rs2108622 CT, rs2231142 GG, rs2279343 AA, rs2306283 AA, rs2740574 TT, rs3093105 AC, rs3211371 CT, rs35599367 GG, rs3745274 GG, rs3892097 CT, rs4149056 TT, rs4680 AA, rs56005131 GG, rs59086055 GG, rs72549306 CC, rs75017182 GG, rs776746 CC, rs78060119 CC, rs8192709 CC, rs9923231 TT rs1045642 GG, rs10509681 TT, rs1801133 AG, rs2032582 CC, rs2108622 CT, rs2740574 TT, rs4149056 TT, rs4680 AA, rs9923231 TT rs1045642 GG, rs10509681 TT, rs1801133 AG, rs2032582 CC, rs2108622 CT, rs2740574 TT, rs4149056 TT, rs4680 AA, rs9923231 TT

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pgx-main/scripts/cyp1a2/hg38/bin/snv_def_modules.py
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@@ -279,7 +279,7 @@ def cand_snv_allele_calling(database, infile, infile_full, infile_full_gt, infil
min_score = min(score)
elif chkList(score) == "Equal":
if chkList(score) == "Equal":
amb_soln_set = []
for elem in tiebreak1:
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]

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pgx-main/var_call.nf
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@@ -224,10 +224,10 @@ if (params.build=='b37') {
debug38 = "--minimum_extract_score_over_homref=0"
if (params.gene=='cyp2d6') {
chrom = "22"
region_a1 = "22:42126000-42137500"
chrom = "chr22"
region_a1 = "chr22:42126000-42137500"
region_a2 = "042126000-042137500"
region_b1 = "22:42126300-42132400"
region_b1 = "chr22:42126300-42132400"
region_b2 = "042126300-042132400"
transcript = "ENST00000645361"