summarize VCF file: chr-pos-ref-alt-refCounts-altCounts-totalCounts
ignore INDELs and positions with multiple alternate alleles
report AF1 (alternate allele frequency)
set AF1 cutoffs to 0.3 and 0.7
require coverage in at least 8 samples
cleanup
merge vcf files, count # of samples a SNP is observed, report SNPs with conflicts
add sample output
remove conflicts from merged SNPs
filter merged SNPs based on # of replicates in which they are observed
determine whether all reads in alignment match ref or alt for given SNP
change observed_cutoff from absolute number to proportion of samples
count skips and bases properly
warn about insufficient coverage
use Capture::Tiny to suppress mpileup output
determine ref vs alt for each polymorphism in a VCF summary file
cleanup
add verbose option
add min ratio cutoff
improve data structure design