I used vscan2vcf.py to convert somatic text (from varscan) output to vcf output by software available at https://github.com/student-t/Varscan2VCF
Input look like :
chrom position ref var normal_reads1 normal_reads2 normal_var_freq normal_gt tumor_reads1 tumor_reads2 tumor_var_freq tumor_gt somatic_status variant_p_value somatic_p_value tumor_reads1_plus tumor_reads1_minus tumor_reads2_plus tumor_reads2_minus normal_reads1_plus normal_reads1_minus normal_reads2_plus normal_reads2_minus
chr1 9061531 A C 288 19 6.19% M 223 10 4.29% M Germline 1.2659658384139693E-9 0.8780075380619026 219 4 10 0 284 4 19 0 chr1 9061537 T G 332 1 0.3% T 247 2 0.8% K Germline 0.12467755803936205 0.3923213650907194 244 3 2 0 332 0 1 0
As a result, I have 25 multiple somatic output vcf files. But when looked sample name, it was missing in each vcf file. VCF header look like
CHROM POS ID REF ALT QUAL FILTER INFO
How can I add sample name in files ?
I will appreciate all the suggestions.
Thanks
