how to manage missing data in vcf file

Question

[evafinegan]

Hello,

I have a multi sample vcf file made by using freebayes:

freebayes -f transcripts.fasta  \
          -L list.txt \
          --targets bed.list   > out.vcf

I have not used any filtering steps and I found that only ~10% of total SNPs are observed in more than half of the samples. Rest are the missing observations as ./.:.:.:.:.:.:.:. Do I need to do any quality filtering or it is something not to worry about? Thank you for any suggestion/help!