After the vcf format file comes out , I want to know the snp site comes from the mother's or father's haplotype.
It is to say which note denotes the +/- the snp site is
Forward/reverse is about strandedness, but I think maybe what you want is phasing information. Have you performed phasing yet?
java -jar GenomeAnalysisTK.jar -T ReadBackedPhasing -R reference.fasta -I reads.bam --variant SNPs.vcf -o phased_SNPs.vcf
use the command, then it is ok? I will try
Yes, that's one of the things you can do to perform phasing.
I would recommend that you look at our presentation documents on phasing here:
If you go to the line that says "Genotype phasing and refinement", there is a pdf presentation and also a link to a video of the live presentation at our workshop in December '12.