Answers.Body: <p>First of all - I would advise you against concluding anything out of your own analysis of the data, you need to consult someone with appropriate training!</p>
  <p>Can you get both? The <code>.bam</code> file is a format that stores information about sequencing reads (usually mapped, but not always). <a href="https://www.metagenomics.wiki/tools/samtools/converting-bam-to-fastq" rel="nofollow noreferrer">You can even extract</a> the original sequencing information from bam files. This is practically the rawest information you can have. The <code>.vcf</code> file is a variant file that gives you some information about inferred variants, but there are plenty of bits of information that will be missing. The basic information regarding sequencing depth and quality of variant calling is still included and therefore most likely sufficient for your physician to see any other variants potentially relevant to your friend's condition.</p>
  <p>I will repeat once again - don't conclude anything on your own. It takes years to gain expertise in analysing genemics data and there is very high risk of misinterpretations if not analysed with care.</p>
  
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Answers.CreationDate: 2022-05-16T17:22:36.817Z
Answers.LastActivityDate: 2022-05-16T17:22:36.817Z
Answers.UserDisplayName: Kamil S Jaron
Body: <p>My friend has a VUS (Polymicrogyria with or without VEDS) mutation that was found in her whole-exome sequencing with respect to the phenotype given that time. At present, her doctors have more information on the complexity and are looking for more explainable mutation present in herself, if any. We asked the company and they're willing to give the raw data.</p>
  <p><strong>Which file format should we opt for?</strong> They've given the option of BAM &amp; VCF.</p>
  
Tags: <sam><vcf><gene><mutations><genetics>
Title: VCF or BAM file for raw data of gene test?
ThreadText: # VCF or BAM file for raw data of gene test?
  
  (Asked by: username_0 on 2022-05-16)
  
  My friend has a VUS (Polymicrogyria with or without VEDS) mutation that was found in her whole-exome sequencing with respect to the phenotype given that time. At present, her doctors have more information on the complexity and are looking for more explainable mutation present in herself, if any. We asked the company and they're willing to give the raw data.
  
  **Which file format should we opt for?** They've given the option of BAM & VCF.
  
  **Tags:** sam, vcf, gene, mutations, genetics
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2022-05-16. Score: 1
  
  First of all - I would advise you against concluding anything out of your own analysis of the data, you need to consult someone with appropriate training!
  
  Can you get both? The `.bam` file is a format that stores information about sequencing reads (usually mapped, but not always). [You can even extract](https://www.metagenomics.wiki/tools/samtools/converting-bam-to-fastq) the original sequencing information from bam files. This is practically the rawest information you can have. The `.vcf` file is a variant file that gives you some information about inferred variants, but there are plenty of bits of information that will be missing. The basic information regarding sequencing depth and quality of variant calling is still included and therefore most likely sufficient for your physician to see any other variants potentially relevant to your friend's condition.
  
  I will repeat once again - don't conclude anything on your own. It takes years to gain expertise in analysing genemics data and there is very high risk of misinterpretations if not analysed with care.
  
  
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