zcat ALL.chrX.BI_Beagle.20100804.genotypes.vcf.gz | grep -v ^## | cut -f 345 | cut -d ':' -f 1 | grep -v '\./\.' | grep -v '|' | head
NA18981 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0
zcat ALL.chrX.BI_Beagle.20100804.genotypes.vcf.gz | grep -v ^## | cut -f 345 | cut -d ':' -f 1 | grep -v '\./\.' | head
NA18981 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0
Is NA18981 phased, or is it not? Is it partially phased? If yes - then what rule/convention explains this partiality? (I know that microsatellite calls are unphased in phased genomes, but I believe I haven't seen any in this file.)
Q2. For somatic chromosomes (I've only checked this on chrs 1 and 2, but I assume this pattern is characteristic for all autosomal chromosomes) all 629 samples appear to be phased - that is, their genotypes at all positions are either unknown
./. or phased (e.g.
0|1). So are all 629 samples really phased on all somatic chromosomes?