Preparing input files for pyclone from Varscan output snp files

[maheshworpaudel5001]

Hello Dear Roth,

Could you help me direct to preparing input files for running pyclone from snp output of VarScan? Here is the content of a snp file.

Native header | VCF field name | Description

chrom | CHROM | Chromosome or reference name position | POS | Position from SAMtools pileup (1-based) ref | REF | Reference base at this position var | ALT | Variant base seen in tumor normal_reads1 | RD (col 10) | Reads supporting reference in normal normal_reads2 | AD (col 10) | Reads supporting variant in normal normal_var_freq | FREQ (col 10) | Variant allele frequency in normal normal_gt | GT (col 10) | Consensus genotype call in normal tumor_reads1 | RD (col 11) | Reads supporting reference in tumor tumor_reads2 | AD (col 11) | Reads supporting variant in tumor tumor_var_freq | FREQ (col 11) | Variant allele frequency in tumor tumor_gt | GT (col 11) | Consensus genotype in tumor somatic_status | SS (col 8) | Somatic status (Germline, Somatic, LOH, Unknown) variant_p_value | GPV (col 8) | Variant p-value from FET for germline events (tumor + normal vs reference) somatic_p_value | SPV (col 8) | Somatic p-value from FET (tumor vs normal) tumor_reads1_plus | DP4 (col 11) | Tumor reference-supporting reads on + strand tumor_reads1_minus |   | Tumor reference-supporting reads on – strand tumor_reads2_plus |   | Tumor variant-supporting reads on + strand tumor_reads2_minus |   | Tumor variant-supporting reads on - strand normal_reads1_plus | DP4 (col 10) | Normal reference-supporting reads on + strand normal_reads1_minus |   | Normal reference-supporting reads on – strand normal_reads2_plus |   | Normal variant-supporting reads on + strand normal_reads2_minus |   | Normal variant-supporting reads on - strand