text: user6505: I would like to know how to convert a pileup file for an adna y chromosome to vcf with Hg19 alignment.
  
  user96: Short answer
  You'll have better luck searching for the term variant calling than with the term converting. A Google search for "variant calling" gives several beginner-level tutorials on the topic. Commonly used tools for variant calling include samtools, GATK, and FreeBayes.
  Long answer
  Converting data files from one format to another is a common task in bioinformatics. But that is not the task you want to perform here—the term convert is misleading.
  A pileup file contains reads aligned to a reference sequence. A VCF file contains a description of putative or validated genetic variant. The process of creating a VCF from alignments is commonly called variant discovery, variant prediction, or variant calling. This is a broad and active area of research interest in bioinformatics, with many available algorithms and tools, each with a different set of parameters and assumptions.
  This forum is not well designed to give you a good introduction to this topic. We are much better equipped to answer specific questions you have about how a particular tool or algorithm works, or why you are observing a particular unexpected result, and so on...assuming you have put in some time to research the question yourself.
  
original_text: 6505: <p>I would like to know how to convert a pileup file for an adna y chromosome to vcf with Hg19 alignment.</p>
   96: <h2>Short answer</h2>
  
  <p>You'll have better luck searching for the term <em><strong>variant calling</strong></em> than with the term <em><strong>converting</strong></em>. A Google search for "variant calling" gives several beginner-level tutorials on the topic. Commonly used tools for variant calling include <a href="http://www.htslib.org/" rel="nofollow noreferrer">samtools</a>, <a href="https://software.broadinstitute.org/gatk/" rel="nofollow noreferrer">GATK</a>, and <a href="https://github.com/ekg/freebayes" rel="nofollow noreferrer">FreeBayes</a>.</p>
  
  <h2>Long answer</h2>
  
  <p>Converting data files from one format to another is a common task in bioinformatics. But that is not the task you want to perform here—the term <em><strong>convert</strong></em> is misleading.</p>
  
  <p>A pileup file contains reads aligned to a reference sequence. A VCF file contains a description of putative or validated genetic variant. The process of creating a VCF from alignments is commonly called <em>variant discovery</em>, <em>variant prediction</em>, or <em>variant calling</em>. This is a broad and active area of research interest in bioinformatics, with many available algorithms and tools, each with a different set of parameters and assumptions.</p>
  
  <p>This forum is not well designed to give you a good introduction to this topic. We are much better equipped to answer specific questions you have about how a particular tool or algorithm works, or why you are observing a particular unexpected result, and so on...assuming you have put in some time to <a href="https://bioinformatics.stackexchange.com/help/how-to-ask">research the question yourself</a>.</p>
  