input CCF data

[wt12318]

Hi,

The Readme indicated that "if you have copy number calls (e.g., from HATCHet), you could correct the read counts to represent the true CCF.". How could I "correct" the read counts to represent the CCF? Similar to this issue (#7)? And if so, the reads of mutation ("if a mutation has 100 reads") should be t_ref_counts + t_alt_counts column in MAF format file? For example, I have a MAF file:

sample  purity  cancer_cell_frac        Chromosome      Start_Position  End_Position    Hugo_Symbol     Variant_Classification  Variant_Type    Reference_Allele        Tumor_Seq_Allele2       t_ref_count     t_alt_count     HGVSp_Short     patient    type    treatment       time    sample2 Tumor_Sample_Barcode
H208682 0.211480023955608       1       chr1    1399081 1399081 CCNL2   Missense_Mutation       SNP     C       T       147     39      p.D76N  Patient7        Tumor tissue    0       2       Patient7-2      Patient7-2
H208682 0.211480023955608       0.32    chr1    1627196 1627196 MIB2    Missense_Mutation       SNP     C       T       154     4       p.R455C Patient7        Tumor tissue    0       2       Patient7-2      Patient7-2

The input for first mutation is ref:93 alt:93 ((147+39)*0.5) and second mutation is ref:133 alt:25 ((154+4)*0.16) ?

Thanks