# xili_sca.csv
Somatic Chromosomal Alteratiosn (SCA)
Somatic copy number and copy neutral loss of heterozygosity calls based off of 
2.5M Illumina SNP arrays using a custom in-house algorithm (based on Li et al, Cancer Prevention Research, 2014).
Note: if chrom, start, end = 0, then this sample did not have any SCA called
using this algorithm.
For samples with some SCA, the chromosomal segments with normal copy number (2 copies without cnLOH) are not listed in this file. Only segments with deviations from the normal control sample are listed. 

# 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 SCA segment
sca_type {smallint} = The call made,
    0 = Double Deletion
    1 = 1-copy loss with B-allele frequency support
    2 = Copy-neutral LOH (CNLOH)
    3 = Baseline 2N (only appears if chrom, start, and end = 0, as noted
        above)
    4 = Unbalanced Gain, with B-allele frequency support
    5 = Balanced Gain
    11 = Apparent 1-copy loss, without B-allele frequency support
    14 = Apparent Unbalanced Gain, without B-allele fequency support.
         Could be Balanced Gain
sca_key {varchar} = SCA types per segment, as text, matching the sca_type
    column, with these mappings:
    sca_type = sca_key
    0 = HomoDel (deletion of both alleles)
    1 = Del (one allele deletion)
    2 = cnLOH (Deletion of one allele and duplication of remaining allele lead to two copies of the same allele).
    3 = Norm (only indicated for samples that have no SCA)
    4 = Gain (unbalanced gain of one or more alleles).
    5 = BalGain (copy gain with same numbers of maternal and paternal alleles). 
    11 = Del_noBAF* (copy number loss without apparent BAF alteration)
    14 = Gain_noBAF** (copy number loss without apparent BAF alteration)
        *Del_noBAF and Del are combined in downstream analyses
        **Gain and Gain_noBAF are combined in downstream analyses



 
  
