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Last pushed: a month ago
Short Description
Dockerized VarDictJava based on anapsix/alpine-java image.
Full Description

Dockerized VarDictJava

VarDictJava is a variant discovery program written in Java and Perl. It is a partial Java port of VarDict variant caller.

Usage:

Docker Pull Command:

docker pull alexcoppe/vardict

Example of single sample mode:

docker run -v $(pwd):/data -v  ~/annotation:/annotation -it --rm alexcoppe/vardict VarDict -G /annotation/hg19.fa -f 0.01 -N sample_1 -b /data/sample_1.bam -z -c 1 -S 2 -E 3 -g 4  /annotation/exome_kit.bed  | docker run -i alexcoppe/vardict teststrandbias.R | docker run -i alexcoppe/vardict var2vcf_valid.pl -N sample_1 -E -f 0.01 > variants.vcf

Example of paired variant calling:

docker run -v $(pwd):/data -v ~/annotation:/annotation -it --rm alexcoppe/vardict VarDict -G /annotation/hg19.fa -f 0.01 -N tumor -b "/data/tumor.bam|/data/normal.bam" -z -c 1 -S 2 -E 3 -g 4  /annotation/exome_kit.bed  | docker run -i alexcoppe/vardict testsomatic.R | docker run -i alexcoppe/vardict var2vcf_paired.pl -N "tumor|normal"  -f 0.01  > variants.vcf
Docker Pull Command
Owner
alexcoppe
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