Fix warning message for annotation exercise

[gaow]

The last step of annotation exercise converting phred scores to float there is a warning that confuses people. because we try to convert . which is missing value, to float, it warns and convert it to missing NA which is correct. Howecer we need a cleaner way to do it so we don't cause confusions -- and also reflect our own good coding practice.

[gaow]

Also in the same exercise i tihnk,

The kinship table EUR_except_FIN.leftnorm.bcftools_qc.vcf_qc.kin0
A list of related individuals depending on the threshold that you provided. In our case we have set a threshold for third-degree relatedness of 0.0625 EUR_except_FIN.leftnorm.bcftools_qc.vcf_qc.related_id

the filenames here are not consistent with what we actually have.