Assuming that you're confident that your VCF is normalised and that you genuinely just want to count occurrences of heterozygous calls per line, then the following will work for either phased (0|1 or 1|0) or unphased (0/1 or 1/0) genotypes, or a mixture of these.
Here, I'm actually accessing a BCF and it's chr1 from 1000 Genomes Phase III data. So, the genotypes are phased. For just un-phased, use gsub(/0\/1|1\/0/,""); for just phased, use gsub(/0\|1|1\|0/,""). the gsub function in AWK conveniently returns the number of matched patterns.
bcftools view chr1.1kg.phase3.v5.bcf | awk -F"\t" 'BEGIN {print "CHR\tPOS\tID\tREF\tALT\tHetCount"} !/^#/ {print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t" gsub(/0\|1|1\|0|0\/1|1\/0/,"")}'
CHR POS ID REF ALT HetCount
1 10177 . A AC 1490
1 10235 . T TA 6
1 10352 rs145072688 T TA 2025
1 10616 rs376342519 CCGCCGTTGCAAAGGCGCGCCG C 35
1 10642 . G A 21
1 11008 . C G 403
1 11012 . C G 403
1 11063 . T G 15
1 13110 . G A 134
1 13116 rs201725126 T G 414
1 13118 rs200579949 A G 414
1 13273 . G C 444
1 13284 . G A 7
1 13380 . C G 41
1 13483 . G C 10
1 13494 . A G 7
1 13550 . G A 17
1 14464 . A T 428
1 14599 . T A 711
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Edit 17th September, 2018:
A modified version for counting on bi-allelic records:
bcftools view test.vcf.gz | \
awk -F"\t" '{line=$0} BEGIN {
print "CHR\tPOS\tID\tREF\tALT\tAltHetCount\tAltHomCount\tRefHomCount"
} !/^#/ {
if (gsub(/,/, ",", $5)==0) {
print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t" gsub(/0\|1|1\|0|0\/1|1\/0/,"") "\t" gsub(/1\/1|1\|1/,"") "\t" gsub(/0\/0|0\|0/,"")
} else if (gsub(/,/, ",", $5)==1) {
print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t" gsub(/1\/0|0\/1|1\|0|0\|1|1\|2|2\|1|1\/2|2\/1/,"")","gsub(/2\/0|0\/2|2\|0|0\|2|1\|2|2\|1|1\/2|2\/1/,"",line) "\t" gsub(/1\/1|1\|1/,"")","gsub(/2\/2|2\|2/,"") "\t" gsub(/0\/0|0\|0/,"")
}
}'
CHR POS ID REF ALT AltHetCount AltHomCount RefHomCount
16 56380495 rs78560610 G A 1 0 10
16 56380502 rs3811361 G A 3 0 8
16 56380570 rs3811360 A G 6 0 5
16 56381544 rs11297695 CT C 6 2 3
16 56381677 . A C 1 0 10
16 56381699 rs11640263 C T 7 2 2
16 56388821 rs148650019 A G 1 0 10
16 56389119 rs143245214 T TTA 3 3 5
16 56389827 rs5817056 CA C 5 1 5
16 56390685 . CTT C,CT 4,9 0,0 1
16 56390968 rs34097380 GA G 4 2 5
16 56396430 rs3748401 C A 1 0 10
16 56396486 rs4924 C T 5 4 2
16 56397153 rs2617846 G A 2 5 3
16 56397174 rs2617847 C G 2 4 3
16 56921684 . T TA,A 3,8 1,1 1
