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VarDict (version 1.8.3+galaxy1)
Restrict SNV calls to the following list of chromosomes (one per line)
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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 other Java based variant callers.

For more information see the VarDict documentation.