text: user14102: When I trying to use bcftools mpileup to convert bam to vcf files,
  I try to use:
  bcftools mpileup -Ob -o resources-broad-hg38-v0-Homo_sapiens_assembly38.fasta.fai input.bam
  
  However, I got this error message:
  [E::fai_build3_core] Failed to open the file resources-broad-hg38-v0-Homo_sapiens_assembly38.fasta.fai
  
  Or, I would get another error message when I use another ref file:
  [E::fai_build_core] Format error, unexpected "c" at line 1
  
  Does anyone know how to solve these problems? Thanks in advance
  Also, could anyone recommend some human gene Reference? The one I am using now is from GATK pipeline (but I don't know if that is good enough).
  The version I am using is:
  Program: bcftools (Tools for variant calling and manipulating VCFs and BCFs)
  License: GNU GPLv3+, due to use of the GNU Scientific Library
  Version: 1.10.2 (using htslib 1.10.2)
  
  
  user73: Regarding a human genome reference, have a look at CHM13/HG002 from the Telomere-to-Telomere consortium:
  https://github.com/marbl/CHM13#assembly-releases
  The benefit of the T2T assembly is that it is fully-assembled across all repetitive regions, which improves the mapping accuracy. The pangenome consortium is working on additional T2T assemblies from other people, trying to capture as much human [structural] variation as possible.
  https://humanpangenome.org/
  The v2.0 assembly, adding chrY from HG002, has only just been released. From the looks of it, it is not yet annotated, but there's gene annotation for all other chromosomes via the v1.1 release:
  https://github.com/marbl/CHM13#downloads
  
original_text: 14102: <p>When I trying to use bcftools mpileup to convert bam to vcf files,
  I try to use:</p>
  <pre><code>bcftools mpileup -Ob -o resources-broad-hg38-v0-Homo_sapiens_assembly38.fasta.fai input.bam
  </code></pre>
  <p>However, I got this error message:</p>
  <pre><code>[E::fai_build3_core] Failed to open the file resources-broad-hg38-v0-Homo_sapiens_assembly38.fasta.fai
  </code></pre>
  <p>Or, I would get another error message when I use another ref file:</p>
  <pre><code>[E::fai_build_core] Format error, unexpected &quot;c&quot; at line 1
  </code></pre>
  <p>Does anyone know how to solve these problems? Thanks in advance</p>
  <p>Also, could anyone recommend some human gene Reference? The one I am using now is from GATK pipeline (but I don't know if that is good enough).</p>
  <p>The version I am using is:</p>
  <pre><code>Program: bcftools (Tools for variant calling and manipulating VCFs and BCFs)
  License: GNU GPLv3+, due to use of the GNU Scientific Library
  Version: 1.10.2 (using htslib 1.10.2)
  </code></pre>
   73: <p>Regarding a human genome reference, have a look at CHM13/HG002 from the Telomere-to-Telomere consortium:</p>
  <p><a href="https://github.com/marbl/CHM13#assembly-releases" rel="nofollow noreferrer">https://github.com/marbl/CHM13#assembly-releases</a></p>
  <p>The benefit of the T2T assembly is that it is fully-assembled across all repetitive regions, which improves the mapping accuracy. The pangenome consortium is working on additional T2T assemblies from other people, trying to capture as much human [structural] variation as possible.</p>
  <p><a href="https://humanpangenome.org/" rel="nofollow noreferrer">https://humanpangenome.org/</a></p>
  <p>The v2.0 assembly, adding chrY from HG002, has only just been released. From the looks of it, it is not yet annotated, but there's gene annotation for all other chromosomes via the v1.1 release:</p>
  <p><a href="https://github.com/marbl/CHM13#downloads" rel="nofollow noreferrer">https://github.com/marbl/CHM13#downloads</a></p>
  