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removing some numbers
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adigenova authored Nov 10, 2021
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## Mesomics (rel2)
## Mesomics

The release2 directory contains 3 subdirectories:


1. **matched**

links to 46 VCFs files of matched tumors.
links to VCFs files of matched tumors.

2. **matched-t-only**

links to 46 VCFs files of matched samples called as t-only.
links to VCFs files of matched samples called as t-only.

3. **t-only**

links to 73 VCFs files of tumor-only samples.
links to VCFs files of tumor-only samples.


The script code/bash/get_mesomics_rel2.sh create the previous file structure.
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The script **jobs/create\_matrix\_rel2.sh**, is a SLURM script that use the singularity container to create the following files:

1. **Somatics.snv.matrix.txt**
Matrix with somatic SNVs (n=203,992)
Matrix with somatic SNVs
2. **Germline.snv.matrix.txt**
Matrix with Germline SNVs (n=694,272)
Matrix with Germline SNVs
3. **Somatics.indel.matrix.txt**
Matrix with somatic INDELs (n=15,727)
Matrix with somatic INDELs
4. **Germline.indel.matrix.txt**
Matrix with Germline INDELs (n=69,969)
Matrix with Germline INDELs

These files are used for training and optimizing the RF classifier.
This job will allocate 50 CPUs in a single machine.
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