Make clearer log-files

[mvvugt]

Log-files are becoming too long and contain a lot of information that is not understood if you don't know the scripts (very well).

For example, in allele_to_vcf.sh, I get a huge log-file because it prints a lot of times: 0 out of x where x stands for the number of gzipped vcf-files created (I think). If you haven't read the script you have no idea that this means and the repetition is useless. Maybe it is more useful to print something only everytime something is actually changing (so if the 0 becomes a 1 for example).

Another example is here, in LoF_annotation.sh, where file names are printed in every loop without explanation or real goal. I understand this might be useful while developing, but as a user this makes things unclear for me. Headers would already help out (such as The following files are used for chromosome ${CHR}) but I think you should even consider removing many of these echo-commands