text: user12683: I have the files of 2 persons that got whole genome sequencing, one by nebula genomics and the other by dante labs.
  
  I want to compare their genomes to see if they are father and son.
  I want to see exactly which genetic sequences they share.
  In the shared sequences, I want to know what mutations exist only in the son.
  
  Which program should I use?
  Each company provide fastq and vcf files to the genome. so I have each genome in fastq and vcf. which is better to use?
  (I have the files on my hard drive, so is it better to use offline program?)
  
  user37: I think you can't do (2) and (3) without the mother.
  (1) is doable to a very high accuracy. It is better to start with fastq. You need to generate a multi-sample VCF first. Here is a high-level overview: a) align reads with bwa-mem; b) sort alignments with samtools and then index the resulting BAM; c) call variants jointly with freebayes (or GATK if you like challenges). After you get the two-sample VCF, you go through every site where the father is homozygous and it is a high-quality site in both samples (e.g. average coverage, high mapping quality, not in difficult regions, etc). Among these sites, check if the child has the paternal allele. If you have a father-son pair, the child is expected to have all the paternal alleles in theory. In practice, if >99% of paternal homozygotes are present in the child, the two samples will almost certainly be a father-son pair. The actual threshold may depend on how you define "high-quality" sites. Errors may lead to apparent mendelian violations.
  In principle, it is possible to do a similar analysis with the two provided VCFs, but you need to be very careful about various technical artifacts.
  
original_text: 12683: <p>I have the files of 2 persons that got whole genome sequencing, one by nebula genomics and the other by dante labs.</p>
  <ol>
  <li>I want to compare their genomes to see if they are father and son.</li>
  <li>I want to see exactly which genetic sequences they share.</li>
  <li>In the shared sequences, I want to know what mutations exist only in the son.</li>
  </ol>
  <p>Which program should I use?</p>
  <p>Each company provide fastq and vcf files to the genome. so I have each genome in fastq and vcf. which is better to use?</p>
  <p>(I have the files on my hard drive, so is it better to use offline program?)</p>
   37: <p>I think you can't do (2) and (3) without the mother.</p>
  <p>(1) is doable to a very high accuracy. It is better to start with fastq. You need to generate a multi-sample VCF first. Here is a high-level overview: a) align reads with bwa-mem; b) sort alignments with samtools and then index the resulting BAM; c) call variants <em>jointly</em> with freebayes (or GATK if you like challenges). After you get the two-sample VCF, you go through every site where the father is homozygous and it is a <em>high-quality</em> site in both samples (e.g. average coverage, high mapping quality, not in difficult regions, etc). Among these sites, check if the child has the paternal allele. If you have a father-son pair, the child is expected to have all the paternal alleles in theory. In practice, if &gt;99% of paternal homozygotes are present in the child, the two samples will almost certainly be a father-son pair. The actual threshold may depend on how you define &quot;high-quality&quot; sites. Errors may lead to apparent mendelian violations.</p>
  <p>In principle, it is possible to do a similar analysis with the two provided VCFs, but you need to be very careful about various technical artifacts.</p>
  