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Update 13_oncoprint_creation.md
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Fixed hg38 -> GRCh38.p7 in filenames
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epartan authored Jun 7, 2024
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4 changes: 2 additions & 2 deletions lessons/13_oncoprint_creation.md
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Expand Up @@ -117,13 +117,13 @@ There are four main parts to the above code:
In order to run the code, we will need to execute:

```
sh VCF_to_oncoprint.sh /n/scratch/users/${USER:0:1}/${USER}/variant_calling/vcf_files/mutect2_syn3_normal_syn3_tumor_hg38-pass-filt-LCR.pedigree_header.snpeff.dbSNP.vcf syn3
sh VCF_to_oncoprint.sh /n/scratch/users/${USER:0:1}/${USER}/variant_calling/vcf_files/mutect2_syn3_normal_syn3_tumor_GRCh38.p7-pass-filt-LCR.pedigree_header.snpeff.dbSNP.vcf syn3
```

We can now inspect our new Oncoprinter formatted text file with:

```
less /n/scratch/users/${USER:0:1}/${USER}/variant_calling/vcf_files/mutect2_syn3_normal_syn3_tumor_hg38-pass-filt-LCR.pedigree_header.snpeff.dbSNP.oncoprint.txt
less /n/scratch/users/${USER:0:1}/${USER}/variant_calling/vcf_files/mutect2_syn3_normal_syn3_tumor_GRCh38.p7-pass-filt-LCR.pedigree_header.snpeff.dbSNP.oncoprint.txt
```

Once you have done this for a given sample, you would use the `cat` command to combine all of your samples together into a single text file. However, we will just be working with a single sample in this example since we don't have access to other samples.
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