Despite the detailed explanation of VCF format on the 1000Genomes site, it is still not clear to me how the data should be interpreted with respect to sample results.
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00002
20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 1|0:48:8:51,51
20 1230237 . T C 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|1:3:5:65,3
For individual NA00002 the vertical upright bar in the second position indicates that the data is phased. But is there any significance as to which side of the bar the digits occur??
Eg for position 14370 does the first digit "1" in "1|0" (>A) relate to a particular parent---mother or father? And the second digit on the right of the bar "0" (>G) indicate the base from the other parent. Similarly at position 1230237 first digit "O" (>T) and second digit to the right of the bar "1" (>C) .
If so then the left chromosome will read AT and the right chromosome GC. Correct? or is it impossible to tell from the order of the alleles with respect to the vertical bar?
thank you in advance