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I would like to know how to convert a pileup file for an adna y chromosome to vcf with Hg19 alignment.

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  • $\begingroup$ Hi @Samir Bouftass, what have you tried so far regarding your question? A quick Google search gave multiple hits, which to me look good quality. I assume you have done so too before posting your question, so what kind of problems did you have with the offered solutions? Can you also edit the title to your question please? In its current from it is rather cryptic. $\endgroup$
    – haci
    Nov 17 '19 at 21:22
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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.

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