awkward

Original command:
bin\cygwin\bin\bash.exe -c "/bin/join -t $'\t' snps.sorted ref.sorted |/bin/sed 's/\///g'|/bin/sort -n -k 3|/bin/awk '{print \"\\\"\"$1\"\\\"\"\",\"\"\\\"\"$2\"\\\"\"\",\"\"\\\"\"$3\"\\\"\"\",\"\"\\\"\"$4\"\\\"\"}' >> out/filtered-autosomal-o37-results.csv"
)

Ported:

join -t $'\t' snps.sorted ref.sorted |sed 's/\///g' |sort -n -k 3 |awk '{print \"\\\"\"$1\"\\\"\"\",\"\"\\\"\"$2\"\\\"\"\",\"\"\\\"\"$3\"\\\"\"\",\"\"\\\"\"$4\"\\\"\"}' >> out/filtered-autosomal-o37-results.csv