get derived allele counts for set of populations (HQ archaics, africans)

derived.awk

#!/usr/bin/awk -f

BEGIN {
	OFS = "\t"
	print "chrom_pos", "ref", "alt", "aa", "da", "Altai", "Denisova3", "Chagyrskaya", "Vindija", "Africa"
}

$4 == $5 {		# chimp matches gorilla
	
	## concatenate African genotypes to a string (columns 10..NF)
	afr = ""
	for(i = 10; i <= NF; i++) {
		afr = afr$i
	}

	## count derived alleles per pop
	## gsub() returns number of replacements in a string
	if ($4 ~ /\./) {		# chimp no data
		
		next

	} else if ($4 ~ /0/) {		# chimp has REF

		aa = $2 # REF
		da = $3 # ALT
		altai = gsub(1, "", $6)
		denis = gsub(1, "", $7)
		chagyr = gsub(1, "", $8)
		vindija = gsub(1, "", $9)
		africa = gsub(1, "", afr)

	} else if ($4 ~ /1/) {		# chimp has ALT
		
		aa = $3 # ALT
		da = $2 # REF
		altai = gsub(0, "", $6)
		denis = gsub(0, "", $7)
		chagyr = gsub(0, "", $8)
		vindija = gsub(0, "", $9)
		africa = gsub(0, "", afr)

	}
	
	print $1,$2,$3, aa, da, altai, denis, chagyr, vindija, africa #, afr

}

Future enhancements

A more robust way to approach this problem would be to provide multiple files to the script, one file per population (with the first one being outgroup, since awk has a simple idiom for treating the first input file differently, i.e. the FNR==NR pattern).

Alternatively, the program could read a popfile defining populations in the data file. This is probably easier to implement, as most of the current logic can stay the same.

Update

The updated script with popfile support is now available in my new repo PopGen.awk.