title: Filtering out DNA repeats with vcftools
body: <p>I am trying to filter out repeats from DNA sequence reads. For this, I have:</p>
  <ul>
  <li><strong>grw_vcf_filtered_2.vcf</strong> as the input file,</li>
  <li><strong>grw_repeatmasker_runner_combined.bed</strong> with the repeat positions I want to filter out</li>
  <li><strong>grw_repeats_removed.vcf</strong> as the output file I will generate.</li>
  </ul>
  <p>However I keep getting the error: <code>grw_repeats_removed.vcf not such file or directory</code> after 4 minutes running.</p>
  <p>Here is my code:</p>
  <pre><code>module load bioinfo-tools vcftools
  
  cd $SNIC_TMP #making temporary file 
  
  cp /proj/snic2020-2-25/nobackup/violeta/grw_vcf_filtered_2.vcf /proj/snic2020-2-25/nobackup/violeta/grw_repeatmasker_runner_combined.bed ./
  
  vcftools --vcf grw_vcf_filtered_2.vcf --out grw_repeats_removed.vcf --exclude-positions grw_repeatmasker_runner_combined.bed
  
  #copy from current location -temporary file- to my directory 
  
  cp ./grw_repeats_removed.vcf /proj/snic2020-2-25/nobackup/violeta/
  </code></pre>