To expand on the comment by Devon Ryan, what you really need are (A.) bam alignment files for each individual and (B.) VCF files for each individual showing all of their genomic variants (with respect to the reference human genome). You mentioned that you had fastq files and that you converted them into fasta files. Do you know if the bam files and VCF files are also available for download anywhere?
If the bam files are not available you will have generate them using sequence aligner software (for example: bwa-mem). With the bam files you can calculate the average depth of coverage (and many other things).
If the VCF files are not available then you will have to generate them from the bam files using variant calling software (for example, the GATK package from the Broad Institute).
In terms of assessing the quality of the sequence runs, a commonly applied tool is name FastQC, but once again, it uses fastq formatted files as input, not fasta files.
The main use for fasta formatted files these days seems to be for compact storage of various reference genomes from different genome sequencing projects (using gzip or similar type of compression).
With the VCF files for each individual in hand you should be able to begin addressing your other questions regarding the frequency of shared variants, etc.