text: user3505: I would like to get some summary statistics on a vcf file from one individual, which has over a million variant calls. I've tried to make a histogram of indel sizes with this command, 
  vcftools --vcf sample.vcf --out sample --hist-indel-len
  
  but it returns an empty file. I see thousands of deletions in the vcf, although strangely no insertions. A typical line in the vcf file I have looks like
  NC_025968.3 168363 191 N <DEL> . . SVTYPE=DEL;STRANDS=+-:19;SVLEN=-1026;END=169389;CIPOS=-9,330;CIEND=-152,9;CIPOS95=-3,61;CIEND95=-32,3;IMPRECISE;SU=19;PE=19;SR=0 GT:SU:PE:SR ./.:19:19:0
  
  Update: I aligned reads to my reference with BWA MEM, then used samblaster to extract discordant pairs and split-reads. I sorted and indexed the three bam files, then used lumpyexpress to generate the vcf.
  samblaster -i sample.sam --excludeDups --addMateTags --maxSplitCount 2 --minNonOverlap 20 | samtools view -S -b - > sample.bam
  
  samtools view -h sample.bam | samblaster -a -e -d sample.disc.sam -s sample.split.sam -o /dev/null
  
  lumpyexpress -B ../sample.sorted.bam -S ../sample.split.sorted.bam -D ../sample.disc.sorted.bam -o sample.vcf 
  
  I would like to see the size distribution of deletions, and if possible, figure out why there are no insertions.
  
  user2085: It looks like lumpy looks for breakpoints in your reference. Presumably places where the is a haplotype switch detectable with the data on-hand?
  My only thought is that since lumpy is being used to produce the VCF file that it is inherently not looking for insertions. I would suggest running the same BAM file through the GATK best practices pipeline (easier said than done) and vcftools pipeline. If those produce insertions but lumpy does not, it must be due to how lumpy produces the calls. Good luck!
  
original_text: 3505: <p>I would like to get some summary statistics on a vcf file from one individual, which has over a million variant calls. I've tried to make a histogram of indel sizes with this command, </p>
  
  <pre><code>vcftools --vcf sample.vcf --out sample --hist-indel-len
  </code></pre>
  
  <p>but it returns an empty file. I see thousands of deletions in the vcf, although strangely no insertions. A typical line in the vcf file I have looks like</p>
  
  <pre><code>NC_025968.3 168363 191 N &lt;DEL&gt; . . SVTYPE=DEL;STRANDS=+-:19;SVLEN=-1026;END=169389;CIPOS=-9,330;CIEND=-152,9;CIPOS95=-3,61;CIEND95=-32,3;IMPRECISE;SU=19;PE=19;SR=0 GT:SU:PE:SR ./.:19:19:0
  </code></pre>
  
  <p>Update: I aligned reads to my reference with BWA MEM, then used samblaster to extract discordant pairs and split-reads. I sorted and indexed the three bam files, then used lumpyexpress to generate the vcf.</p>
  
  <pre><code>samblaster -i sample.sam --excludeDups --addMateTags --maxSplitCount 2 --minNonOverlap 20 | samtools view -S -b - &gt; sample.bam
  
  samtools view -h sample.bam | samblaster -a -e -d sample.disc.sam -s sample.split.sam -o /dev/null
  
  lumpyexpress -B ../sample.sorted.bam -S ../sample.split.sorted.bam -D ../sample.disc.sorted.bam -o sample.vcf 
  </code></pre>
  
  <p>I would like to see the size distribution of deletions, and if possible, figure out why there are no insertions.</p>
   2085: <p>It looks like <code>lumpy</code> <a href="https://github.com/arq5x/lumpy-sv" rel="nofollow noreferrer">looks for breakpoints in your reference</a>. Presumably places where the is a haplotype switch detectable with the data on-hand?</p>
  
  <p>My only thought is that since <code>lumpy</code> is being used to produce the VCF file that it is inherently not looking for insertions. I would suggest running the same BAM file through the GATK best practices pipeline (easier said than done) and vcftools pipeline. If those produce insertions but <code>lumpy</code> does not, it must be due to how <code>lumpy</code> produces the calls. Good luck!</p>
  