Quick Start - LiuJie1117/MesKit GitHub Wiki
Prepare input files
To analyse with our packages you need to provide a set of input files, including:
- Necessary details of samples;
- Mutation information (MAF files);
- Output files of Pyclone analysis (ccf files).
Here we give examples of details of samples and MAF files. And others you should prepare contain the output tables of Pyclone analysis (clusters.tsv and loci.tsv for cluster and locus specific information).
Information of samples
It should contain the sampleID, patientID, lesion and time.
| sample | patient | lesion | time |
|---|---|---|---|
| 311252-S | 311252 | S | - |
| 311252-V | 311252 | V | - |
| 311252-TC1 | 311252 | TC | - |
| 311252-TC2 | 311252 | TC | - |
The MAF files
| Hugo_Symbol | Chromosome | Start_Position | End_Position | Variant_Classification | Variant_Type | Reference_Allele | Tumor_Seq_Allele1 | Tumor_Seq_Allele2 | Ref_allele_depth | Alt_allele_depth | VAF | CDS_Change | Protein_Change | Tumor_Sample_Barcode |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| LOC729737 | 1 | 135207 | 135207 | RNA | SNP | C | C | G | 40 | 4 | 0.0909 | NA | NA | 311252-S |
| TTC34,ACTRT2 | 1 | 2869474 | 2869474 | IGR | INS | - | CTCTCT | 43 | 8 | 0.1568 | NA | NA | 311252-S | |
| NBPF1 | 1 | 16908223 | 16908223 | Intron | SNP | T | T | A | 142 | 8 | 0.0533 | NA | NA | 311252-S |
| PRAMEF2 | 1 | 12921600 | 12921600 | Missense_Mutation | SNP | C | C | T | 73 | 3 | 0.0394 | c.C1391T | p.P464L | 311252-S |