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.

Added page on bcftools

• Added page on bcftools: docs/bcftools.md
• Added section on samtools faidx to samtools.md
• Added section on BCF format to file_formats.md
• Updated links to Program guides in README.md

Release with DOI.

v1.0.1

Updated repository structure on README.md

Initial release

Initial release of bioinfo-notebook.