Fixed file paths and names in SNP calling scripts.

• In scripts/annotated_snps_filter.R, fixed the setwd() command on line
  35, working directory is now set as ~/bioinfo-notebook/data.
• In scripts/annotating_snps.R, the variable output_name on line 33 is
  now used to name the output file on line 94.
• In scripts/snp_calling.sh, the cd command on line 98 now changes
  the working directory to ~/bioinfo-notebook/data.