Incorrect TCS calculation in .vcf.gz file due to bug

[tobyaicher]

Hi,

I was comparing the .vcf.gz and _subclones.txt outputs of Battenberg and noticed a discrepancy in the second state copy numbers. Specifically, it appears that when you add up the major and minor alleles of the second copy number state in the _subclones.txt file it does not equal the TCS field of the .vcf.gz file.

I looked in the code here:
https://github.com/cancerit/cgpBattenberg/blob/dev/perl/bin/battenberg_CN_to_VCF.pl

I found that it is because the code here:
$mt_cn_tot_sec = $mt_cn_maj + $mt_cn_min;

It is calculating mt_cn_tot_sec from the major and minor allele copy numbers of the FIRST copy number state, when it should be calculated using the second copy number state like this:
$mt_cn_tot_sec = $mt_cn_maj_sec + $mt_cn_min_sec;

Thanks