VarDict

VarDict is a sensitive variant caller for both single and paired sample variant calling from BAM files. VarDict implements several novel features such as amplicon bias aware variant calling from targeted sequencing experiments, rescue of long indels by realigning bwa soft clipped reads and better scalability than Java based variant callers.

Code by Zhongwu Lai 2014.

Requirements

• Perl (uses /usr/bin/env perl)
• R (uses /usr/bin/env R)
• samtools (must be in path)

Quick start

Make sure the VarDict folder (scripts vardict.pl, vardict, testsomatic.R, teststrandbias.R, var2vcf_valid.pl and var2vcf_somatic.pl) is in path before running the following commands.

• Running in single sample mode:

  AF_THR="0.01" # minimum allele frequency
  vardict -G /path/to/hg19.fa -f $AF_THR -N sample_name -b /path/to/my.bam -z -F -c 1 -S 2 -E 3 -g 4 /path/to/my.bed | teststrandbias.R | var2vcf_valid.pl -N sample_name -E -f $AF_THR
  

• Paired variant calling:

  AF_THR="0.01" # minimum allele frequency
  vardict -G /path/to/hg19.fa -f $AF_THR -N tumor_sample_name -b "/path/to/tumor.bam|/path/to/normal.bam" -z -F -c 1 -S 2 -E 3 -g 4 /path/to/my.bed | testsomatic.R | var2vcf_somatic.pl -N "tumor_sample_name|normal_sample_name" -f $AF_THR
  

Contributors

• Zhongwu Lai, AstraZeneca

• Miika Ahdesmaki, AstraZeneca

• Brad Chapman, Harvard School of Public Health

License

The code is freely available under the MIT license.