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Edward WangEdward Wang
Edward Wang
authored and
Edward Wang
committed
update ReadMe
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‎README.md

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@@ -8,37 +8,9 @@ HgvsGo was specifically developed for clinical use, making it well-suited for me
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## How to Use HgvsGo
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### Step 1: Download the Repository and Build HgvsGo
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```
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git clone https://github.com/SoloEdward/HgvsGo.git
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cd ./HgvsGo/src/
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mkdir build
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cd build/
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cmake ..
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make
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cd ../../
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```
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### Step 2: Download and Prepare the Human Genome
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```
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wget https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.fna.gz
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gunzip GRCh37_latest_genomic.fna.gz
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python parse_genome.py
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```
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### Step 3: Download RNA Sequences for All Transcripts
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```
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wget https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_rna.fna.gz
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gunzip GRCh37_latest_rna.fna.gz
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```
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### Step 4: Run the Program
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```
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./src/build/HgvsGo ./GRCh37_latest_rna.fna.gz ./human.genome.fa ./refseq.select.hg19.parsed.txt demo.input.txt demo.output.txt
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apptainer run HgvsGo.hg19.sif demo.input.txt demo.output.txt
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apptainer run HgvsGo.hg38.sif demo.hg38.input.txt demo.hg38.output.txt
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```
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## Input Format

‎demo.hg38.input.txt

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chrom pos ref alt
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7 55154121 C T
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7 55155858 G A
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7 55155858 G C
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7 55163790 G C
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7 55170317 G T
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7 55174790 ATCTCCGAAAGCCAACAAGGAAATC A
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7 55181377 A T
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7 55181379 G A
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7 55181379 G T
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7 55191821 C T
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7 55191821 CT AG
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7 55191822 T A
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7 55191822 TG GT
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7 55191823 G T
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7 55191858 A G
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7 55192790 G T
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7 55192858 A T
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7 55198790 C T
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7 55200325 T C
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7 55200325 T G

‎demo.hg38.output.txt

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chrom pos ref alt transcript_id gene exon_id hgvs_c hgvs_p
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7 55154121 C T NM_005228.5 EGFR 7 c.858C>T p.Ser286=
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7 55154121 C T NM_001346899.2 EGFR 6 c.723C>T p.Ser241=
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7 55154121 C T NM_001346941.2 EGFR 2 c.89-1709C>T NA
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7 55154121 C T NM_001346898.2 EGFR 7 c.858C>T p.Ser286=
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7 55154121 C T NM_001346897.2 EGFR 6 c.723C>T p.Ser241=
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7 55154121 C T NM_201284.2 EGFR 7 c.858C>T p.Ser286=
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7 55154121 C T NM_201282.2 EGFR 7 c.858C>T p.Ser286=
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7 55154121 C T NM_201283.2 EGFR 7 c.858C>T p.Ser286=
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7 55154121 C T NM_001346900.2 EGFR 7 c.699C>T p.Ser233=
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7 55155858 G A NM_005228.5 EGFR 8 c.918G>A p.Ser306=
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7 55155858 G A NM_001346899.2 EGFR 7 c.783G>A p.Ser261=
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7 55155858 G A NM_001346941.2 EGFR 2 c.117G>A p.Ser39=
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7 55155858 G A NM_001346898.2 EGFR 8 c.918G>A p.Ser306=
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7 55155858 G A NM_001346897.2 EGFR 7 c.783G>A p.Ser261=
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7 55155858 G A NM_201284.2 EGFR 8 c.918G>A p.Ser306=
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7 55155858 G A NM_201282.2 EGFR 8 c.918G>A p.Ser306=
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7 55155858 G A NM_201283.2 EGFR 8 c.918G>A p.Ser306=
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7 55155858 G A NM_001346900.2 EGFR 8 c.759G>A p.Ser253=
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7 55155858 G C NM_005228.5 EGFR 8 c.918G>C p.Ser306=
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7 55155858 G C NM_001346899.2 EGFR 7 c.783G>C p.Ser261=
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7 55155858 G C NM_001346941.2 EGFR 2 c.117G>C p.Ser39=
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7 55155858 G C NM_001346898.2 EGFR 8 c.918G>C p.Ser306=
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7 55155858 G C NM_001346897.2 EGFR 7 c.783G>C p.Ser261=
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7 55155858 G C NM_201284.2 EGFR 8 c.918G>C p.Ser306=
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7 55155858 G C NM_201282.2 EGFR 8 c.918G>C p.Ser306=
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7 55155858 G C NM_201283.2 EGFR 8 c.918G>C p.Ser306=
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7 55155858 G C NM_001346900.2 EGFR 8 c.759G>C p.Ser253=
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7 55163790 G C NM_005228.5 EGFR 14 c.1689G>C p.Leu563=
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7 55163790 G C NM_001346899.2 EGFR 13 c.1554G>C p.Leu518=
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7 55163790 G C NM_001346941.2 EGFR 8 c.888G>C p.Leu296=
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7 55163790 G C NM_001346898.2 EGFR 14 c.1689G>C p.Leu563=
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7 55163790 G C NM_001346897.2 EGFR 13 c.1554G>C p.Leu518=
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7 55163790 G C NM_201284.2 EGFR 14 c.1689G>C p.Leu563=
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7 55163790 G C NM_201282.2 EGFR 14 c.1689G>C p.Leu563=
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7 55163790 G C NM_001346900.2 EGFR 14 c.1530G>C p.Leu510=
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7 55170317 G T NM_005228.5 EGFR 16 c.1881-858G>T NA
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7 55170317 G T NM_001346899.2 EGFR 15 c.1746-858G>T NA
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7 55170317 G T NM_001346941.2 EGFR 10 c.1080-858G>T NA
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7 55170317 G T NM_001346898.2 EGFR 16 c.1881-858G>T NA
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7 55170317 G T NM_001346897.2 EGFR 15 c.1746-858G>T NA
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7 55170317 G T NM_201284.2 EGFR 16 c.1891G>T p.Glu631Ter
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7 55170317 G T NM_001346900.2 EGFR 16 c.1722-858G>T NA
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7 55174790 ATCTCCGAAAGCCAACAAGGAAATC A NM_005228.5 EGFR 19 c.2254_2277del p.Ser752_Ile759del
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7 55174790 ATCTCCGAAAGCCAACAAGGAAATC A NM_001346899.2 EGFR 18 c.2119_2142del p.Ser707_Ile714del
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7 55174790 ATCTCCGAAAGCCAACAAGGAAATC A NM_001346941.2 EGFR 13 c.1453_1476del p.Ser485_Ile492del
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7 55174790 ATCTCCGAAAGCCAACAAGGAAATC A NM_001346898.2 EGFR 19 c.2254_2277del p.Ser752_Ile759del
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7 55174790 ATCTCCGAAAGCCAACAAGGAAATC A NM_001346897.2 EGFR 18 c.2119_2142del p.Ser707_Ile714del
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7 55174790 ATCTCCGAAAGCCAACAAGGAAATC A NM_001346900.2 EGFR 19 c.2095_2118del p.Ser699_Ile706del
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7 55181377 A T NM_005228.5 EGFR 20 c.2368A>T p.Thr790Ser
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7 55181377 A T NM_001346899.2 EGFR 19 c.2233A>T p.Thr745Ser
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7 55181377 A T NM_001346941.2 EGFR 14 c.1567A>T p.Thr523Ser
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7 55181377 A T NM_001346898.2 EGFR 20 c.2368A>T p.Thr790Ser
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7 55181377 A T NM_001346897.2 EGFR 19 c.2233A>T p.Thr745Ser
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7 55181377 A T NM_001346900.2 EGFR 20 c.2209A>T p.Thr737Ser
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7 55181379 G A NM_005228.5 EGFR 20 c.2370G>A p.Thr790=
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7 55181379 G A NM_001346899.2 EGFR 19 c.2235G>A p.Thr745=
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7 55181379 G A NM_001346941.2 EGFR 14 c.1569G>A p.Thr523=
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7 55181379 G A NM_001346898.2 EGFR 20 c.2370G>A p.Thr790=
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7 55181379 G A NM_001346897.2 EGFR 19 c.2235G>A p.Thr745=
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7 55181379 G A NM_001346900.2 EGFR 20 c.2211G>A p.Thr737=
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7 55181379 G T NM_005228.5 EGFR 20 c.2370G>T p.Thr790=
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7 55181379 G T NM_001346899.2 EGFR 19 c.2235G>T p.Thr745=
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7 55181379 G T NM_001346941.2 EGFR 14 c.1569G>T p.Thr523=
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7 55181379 G T NM_001346898.2 EGFR 20 c.2370G>T p.Thr790=
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7 55181379 G T NM_001346897.2 EGFR 19 c.2235G>T p.Thr745=
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7 55181379 G T NM_001346900.2 EGFR 20 c.2211G>T p.Thr737=
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7 55191821 C T NM_005228.5 EGFR 21 c.2572C>T p.Leu858=
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7 55191821 C T NM_001346899.2 EGFR 20 c.2437C>T p.Leu813=
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7 55191821 C T NM_001346941.2 EGFR 15 c.1771C>T p.Leu591=
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7 55191821 C T NM_001346898.2 EGFR 21 c.2572C>T p.Leu858=
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7 55191821 C T NM_001346897.2 EGFR 20 c.2437C>T p.Leu813=
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7 55191821 C T NM_001346900.2 EGFR 21 c.2413C>T p.Leu805=
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7 55191821 CT AG NM_005228.5 EGFR 21 c.2572_2573inv p.Leu858Arg
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7 55191821 CT AG NM_001346899.2 EGFR 20 c.2437_2438inv p.Leu813Arg
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7 55191821 CT AG NM_001346941.2 EGFR 15 c.1771_1772inv p.Leu591Arg
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7 55191821 CT AG NM_001346898.2 EGFR 21 c.2572_2573inv p.Leu858Arg
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7 55191821 CT AG NM_001346897.2 EGFR 20 c.2437_2438inv p.Leu813Arg
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7 55191821 CT AG NM_001346900.2 EGFR 21 c.2413_2414inv p.Leu805Arg
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7 55191822 T A NM_005228.5 EGFR 21 c.2573T>A p.Leu858Gln
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7 55191822 T A NM_001346899.2 EGFR 20 c.2438T>A p.Leu813Gln
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7 55191822 T A NM_001346941.2 EGFR 15 c.1772T>A p.Leu591Gln
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7 55191822 T A NM_001346898.2 EGFR 21 c.2573T>A p.Leu858Gln
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7 55191822 T A NM_001346897.2 EGFR 20 c.2438T>A p.Leu813Gln
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7 55191822 T A NM_001346900.2 EGFR 21 c.2414T>A p.Leu805Gln
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7 55191822 TG GT NM_005228.5 EGFR 21 c.2573_2574delinsGT p.Leu858Arg
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7 55191822 TG GT NM_001346899.2 EGFR 20 c.2438_2439delinsGT p.Leu813Arg
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7 55191822 TG GT NM_001346941.2 EGFR 15 c.1772_1773delinsGT p.Leu591Arg
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7 55191822 TG GT NM_001346898.2 EGFR 21 c.2573_2574delinsGT p.Leu858Arg
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7 55191822 TG GT NM_001346897.2 EGFR 20 c.2438_2439delinsGT p.Leu813Arg
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7 55191822 TG GT NM_001346900.2 EGFR 21 c.2414_2415delinsGT p.Leu805Arg
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7 55191823 G T NM_005228.5 EGFR 21 c.2574G>T p.Leu858=
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7 55191823 G T NM_001346899.2 EGFR 20 c.2439G>T p.Leu813=
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7 55191823 G T NM_001346941.2 EGFR 15 c.1773G>T p.Leu591=
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7 55191823 G T NM_001346898.2 EGFR 21 c.2574G>T p.Leu858=
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7 55191823 G T NM_001346897.2 EGFR 20 c.2439G>T p.Leu813=
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7 55191823 G T NM_001346900.2 EGFR 21 c.2415G>T p.Leu805=
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7 55191858 A G NM_005228.5 EGFR 21 c.2609A>G p.His870Arg
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7 55191858 A G NM_001346899.2 EGFR 20 c.2474A>G p.His825Arg
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7 55191858 A G NM_001346941.2 EGFR 15 c.1808A>G p.His603Arg
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7 55191858 A G NM_001346898.2 EGFR 21 c.2609A>G p.His870Arg
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7 55191858 A G NM_001346897.2 EGFR 20 c.2474A>G p.His825Arg
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7 55191858 A G NM_001346900.2 EGFR 21 c.2450A>G p.His817Arg
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7 55192790 G T NM_005228.5 EGFR 22 c.2650G>T p.Glu884Ter
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7 55192790 G T NM_001346899.2 EGFR 21 c.2515G>T p.Glu839Ter
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7 55192790 G T NM_001346941.2 EGFR 16 c.1849G>T p.Glu617Ter
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7 55192790 G T NM_001346898.2 EGFR 22 c.2650G>T p.Glu884Ter
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7 55192790 G T NM_001346897.2 EGFR 21 c.2515G>T p.Glu839Ter
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7 55192790 G T NM_001346900.2 EGFR 22 c.2491G>T p.Glu831Ter
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7 55192858 A T NM_005228.5 EGFR 22 c.2701+17A>T NA
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7 55192858 A T NM_001346899.2 EGFR 21 c.2566+17A>T NA
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7 55192858 A T NM_001346941.2 EGFR 16 c.1900+17A>T NA
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7 55192858 A T NM_001346898.2 EGFR 22 c.2701+17A>T NA
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7 55192858 A T NM_001346897.2 EGFR 21 c.2566+17A>T NA
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7 55192858 A T NM_001346900.2 EGFR 22 c.2542+17A>T NA
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7 55198790 C T NM_005228.5 EGFR 23 c.2775C>T p.Ser925=
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7 55198790 C T NM_001346899.2 EGFR 22 c.2640C>T p.Ser880=
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7 55198790 C T NM_001346941.2 EGFR 17 c.1974C>T p.Ser658=
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7 55198790 C T NM_001346898.2 EGFR 23 c.2775C>T p.Ser925=
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7 55198790 C T NM_001346897.2 EGFR 22 c.2640C>T p.Ser880=
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7 55198790 C T NM_001346900.2 EGFR 23 c.2616C>T p.Ser872=
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7 55200325 T C NM_005228.5 EGFR 24 c.2858T>C p.Ile953Thr
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7 55200325 T C NM_001346899.2 EGFR 23 c.2723T>C p.Ile908Thr
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7 55200325 T C NM_001346941.2 EGFR 18 c.2057T>C p.Ile686Thr
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7 55200325 T C NM_001346898.2 EGFR 24 c.2858T>C p.Ile953Thr
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7 55200325 T C NM_001346897.2 EGFR 23 c.2723T>C p.Ile908Thr
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7 55200325 T C NM_001346900.2 EGFR 24 c.2699T>C p.Ile900Thr
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7 55200325 T G NM_005228.5 EGFR 24 c.2858T>G p.Ile953Arg
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7 55200325 T G NM_001346899.2 EGFR 23 c.2723T>G p.Ile908Arg
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7 55200325 T G NM_001346941.2 EGFR 18 c.2057T>G p.Ile686Arg
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7 55200325 T G NM_001346898.2 EGFR 24 c.2858T>G p.Ile953Arg
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7 55200325 T G NM_001346897.2 EGFR 23 c.2723T>G p.Ile908Arg
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7 55200325 T G NM_001346900.2 EGFR 24 c.2699T>G p.Ile900Arg

‎parse_genome.py

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