# pASCAT_SCA.csv
Somatic Chromosomal Alterations (SCA)
Chromosome copy number and copy neutral loss of heterozygosity calls based off
of 2.5M Illumina SNP arrays using a modified version of the ASCAT algorithm.

# Columns:
DNANum {varchar} = DNANumber identifying unique samples to tie with other
    data tables
chrom {integer} = The integer chromosome number
start/end {integer} = The start/stop coordinates of each copy number segment
rawA/rawB {double} = The fractional copy number per allele.
intA/intB {integer} = integer copy number of each allele. This is the
    verified copy number call made (not a simple rounding of rawA/rawB),
    so give preference to these columns (see methods).
copynum {double} = The total fractional copy number for the segment
sca_key {varchar} = SCA type per segment, matching call categories made in custom xili
    calling algorithm.  Field values are: 
        HomoDel = loss of both alleles
        Del = deletion of one allele
        cnLOH = 2 copies of only one allele
        Norm = 1 copy of each allele
        Gain = imbalance between two alleles, where at least one allele is more
            than 1 copy
        BalGain = both alleles have same number of copies, both > 1 copy
        HighGain = 6 or more copies

