text: user2621: I have NGS illumina RNA-seq reads from M. musculus (mm10). I am trying to find variants along the strand portion of the reads in the refseq (mm10).
  I mapped a pair of sequence files and generated a BAM file. Now I need to generate a VCF file from this BAM file. I’ve checked Galaxy for direct tools, but I couldn’t identify one. Any suggestions on how to turn a BAM file into VCF? Thank you in advance.
  
  user294: You can use Freebayes, provided you have your BAM file and the reference genome.
  Example:
  freebayes -f genome.fa aln.bam > var.vcf
  
  I'd suggest you go through the whole github documentation, and choose the option(s) more suitable for your needs (ploidy, read support, etc.)
  
  user57: It's not really possible to convert bam to vcf. bam is a mapping file, it does not contain the information about variants, this information needs to be inferred in process called variant calling. I find important to mention that it's not just a different format of the same thing.
  How to call variants (a vcf file) from mapped reads (a bam file) is very broad question, it depends on the sequencing technology (Illumina, PacBio, ...), the type of sequencing (whole genome sequencing, RAD, RNA-seq, ...), the sampling (calling of individuals vs population variability), the quality of a reference (human vs denovo assembly made by a postdoc in your lab)... For a lot of cases the answer is simply GATK, partially because it has well written manual, but mainly just because many people use it.
  Some more detailed cases are well answered in more specific questions :
  
  How do I generate a variant list (i.e. VCF file) using Illumina reads from a human genome?
  Somatic tumor only variant calling?
  Why are there missing calls in a VCF file from exome sequencing?
  
  
original_text: 2621: <p>I have NGS illumina RNA-seq reads from <em>M. musculus</em> (mm10). I am trying to find variants along the strand portion of the reads in the refseq (mm10).</p>
  
  <p>I mapped a pair of sequence files and generated a BAM file. Now I need to generate a VCF file from this BAM file. I’ve checked Galaxy for direct tools, but I couldn’t identify one. Any suggestions on how to turn a BAM file into VCF? Thank you in advance.</p>
   294: <p>You can use <a href="https://github.com/ekg/freebayes" rel="noreferrer">Freebayes</a>, provided you have your BAM file and the reference genome.</p>
  
  <p>Example:</p>
  
  <pre><code>freebayes -f genome.fa aln.bam &gt; var.vcf
  </code></pre>
  
  <p>I'd suggest you go through the whole github documentation, and choose the option(s) more suitable for your needs (ploidy, read support, etc.)</p>
   57: <p>It's not really possible to <strong>convert</strong> <code>bam</code> to <code>vcf</code>. <code>bam</code> is a mapping file, it does not contain the information about variants, this information needs to be inferred in process called variant calling. I find important to mention that it's not just a different format of the same thing.</p>
  
  <p>How to <strong>call variants</strong> (a <code>vcf</code> file) from mapped reads (a <code>bam</code> file) is very broad question, it depends on the sequencing technology (Illumina, PacBio, ...), the type of sequencing (whole genome sequencing, RAD, RNA-seq, ...), the sampling (calling of individuals vs population variability), the quality of a reference (human vs denovo assembly made by a postdoc in your lab)... For a lot of cases the answer is simply <a href="https://software.broadinstitute.org/gatk/" rel="noreferrer">GATK</a>, partially because it has well written manual, but mainly just because many people use it.</p>
  
  <p>Some more detailed cases are well answered in more specific questions :</p>
  
  <ul>
  <li><a href="https://bioinformatics.stackexchange.com/questions/654/how-do-i-generate-a-variant-list-i-e-vcf-file-using-illumina-reads-from-a-hum">How do I generate a variant list (i.e. VCF file) using Illumina reads from a human genome?</a></li>
  <li><a href="https://bioinformatics.stackexchange.com/questions/2744/somatic-tumor-only-variant-calling">Somatic tumor only variant calling?</a></li>
  <li><a href="https://bioinformatics.stackexchange.com/questions/672/why-are-there-missing-calls-in-a-vcf-file-from-exome-sequencing">Why are there missing calls in a VCF file from exome sequencing?</a></li>
  </ul>
  