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 many Java based variant callers.
A Java based drop-in replacement for vardict.pl is being developed at https://github.com/AstraZeneca-NGS/VarDictJava. The Java implementation is approximately 10 times faster than the original Perl implementation and does removes dependency on samtools
To enable amplicon aware variant calling (single sample mode only; not supported in paired variant calling), please make sure the bed file has 8 columns with the 7th and 8th columns containing the insert interval (therefore subset of the 2nd and 3rd column interval).
VarDict is fully integrated in e.g. bcbio-nextgen, see https://github.com/chapmanb/bcbio-nextgen
Code by Zhongwu Lai 2014.
- Perl (uses /usr/bin/env perl)
- R (uses /usr/bin/env R)
- samtools (must be in path, not required if using the Java implementation in place of vardict.pl)
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 -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" -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
- Zhongwu Lai, AstraZeneca
- Miika Ahdesmaki, AstraZeneca
- Brad Chapman, Harvard School of Public Health
The code is freely available under the MIT license.