Dockerized VarDictJava based on anapsix/alpine-java image.
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VarDictJava is a variant discovery program written in Java and Perl. It is a partial Java port of VarDict variant caller.
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
Content type
Image
Digest
Size
373.6 MB
Last updated
over 6 years ago
docker pull alexcoppe/vardict