Bash script to parse MAF (minor allele frequency) for minor allele (second most frequent allele) from VCFtools .frq files.

parse_maf.sh

#!/bin/bash

sed 1d $1 | while read line
do
  CHROM=`echo $line | awk '{print $1}'`
  POS=`echo $line | awk '{print $2}'`

  num_alleles=`echo $line | awk '{print $3}'`
  num_chroms=`echo $line | awk '{print $4}'`
  mafs=()
  for i in `seq 1 $num_alleles`; do
        col=$(($i + 4))
        mafs+=(`echo $line | awk -v col=$col '{print $col}' | awk -F ":" '{print $2}'`)
  done
  IFS=$'\n' sorted=($(sort -gr <<< "${mafs[*]}"))
  unset IFS

  re=".*[[:space:]]([ACGT]*:)(${sorted[1]}).*"
  if [[ $line =~ $re ]]; then
    MAF=`echo ${BASH_REMATCH[1]}${BASH_REMATCH[2]}`
  fi
  echo "$CHROM $POS $num_alleles $num_chroms $MAF"

done