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Quick Start
LiuJie1117 edited this page May 28, 2019
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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).
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 | - |
| 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 |