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Merge pull request #775 from kittychaseNC/master
update freebayes1.3.7
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| FROM ubuntu:jammy as builder | ||
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| ARG FREEBAYES_VER="1.3.7" | ||
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| ARG DEBIAN_FRONTEND=noninteractive | ||
| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| ca-certificates \ | ||
| build-essential \ | ||
| pkg-config \ | ||
| meson \ | ||
| cmake \ | ||
| zlib1g-dev \ | ||
| liblzma-dev \ | ||
| libbz2-dev \ | ||
| libncurses5-dev \ | ||
| libc6 \ | ||
| libgcc-s1 \ | ||
| libstdc++6 \ | ||
| libvcflib1 \ | ||
| libvcflib-tools \ | ||
| libseqlib-dev \ | ||
| libvcflib-dev \ | ||
| bc \ | ||
| parallel \ | ||
| ninja-build \ | ||
| wget \ | ||
| samtools \ | ||
| vcftools && \ | ||
| rm -rf /var/lib/apt/lists/* && apt-get autoclean | ||
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| RUN wget https://github.com/freebayes/freebayes/archive/refs/tags/v${FREEBAYES_VER}.tar.gz && \ | ||
| tar -xvzf v${FREEBAYES_VER}.tar.gz && \ | ||
| mv freebayes-${FREEBAYES_VER} /freebayes && \ | ||
| cd /freebayes && \ | ||
| meson build/ && \ | ||
| cd build && \ | ||
| ninja | ||
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| RUN /freebayes/build/freebayes --help | ||
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| FROM ubuntu:jammy as app | ||
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| LABEL base.image="ubuntu:focal" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="FreeBayes" | ||
| LABEL software.version="1.3.7" | ||
| LABEL description="FreeBayes is a haplotype-based variant detector and is a great tool for calling variants from a population." | ||
| LABEL website="https://github.com/freebayes/freebayes" | ||
| LABEL license="https://github.com/freebayes/freebayes/blob/master/LICENSE" | ||
| LABEL maintainer="Kitty Chase" | ||
| LABEL maintainer.email="[email protected]" | ||
| LABEL maintainer2="Jill Hagey" | ||
| LABEL maintainer2.email="[email protected]" | ||
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| COPY --from=builder /freebayes/build/* /usr/local/bin/ | ||
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| # vcftools version is 0.1.16 | ||
| # samtools version is 1.13 | ||
| ARG DEBIAN_FRONTEND=noninteractive | ||
| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| bc \ | ||
| ca-certificates \ | ||
| libseqlib-dev \ | ||
| libvcflib-tools \ | ||
| parallel \ | ||
| procps \ | ||
| samtools \ | ||
| vcftools \ | ||
| wget && \ | ||
| rm -rf /var/lib/apt/lists/* && apt-get autoclean | ||
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| RUN freebayes --help && vcftools --help && samtools --help | ||
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| ENV LC_ALL=C | ||
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| WORKDIR /data | ||
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| CMD freebayes --help | ||
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| # new base for testing | ||
| FROM app as test | ||
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| RUN freebayes --help && vcftools --help && samtools --help | ||
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| RUN wget -q https://github.com/StaPH-B/docker-builds/raw/master/tests/SARS-CoV-2/SRR13957123.sorted.bam && \ | ||
| wget -q https://raw.githubusercontent.com/UPHL-BioNGS/Cecret/master/genomes/MN908947.3.fasta && \ | ||
| freebayes -f MN908947.3.fasta SRR13957123.sorted.bam > var.vcf && \ | ||
| head var.vcf |
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| # FreeBayes Container | ||
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| ## Documentation and Overview | ||
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| Main Tool: FreeBayes - [Haplotype-based variant detection from short-read sequencing](https://arxiv.org/abs/1207.3907) | ||
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| Additional tools: | ||
| - vcftools version is 0.1.16 | ||
| - samtools version is 1.13 | ||
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| Full documentation: https://github.com/freebayes/freebayes | ||
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| FreeBayes is a haplotype-based variant detector and is a great tool for calling variants from a population. | ||
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| FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. | ||
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| FreeBayes is haplotype-based, in the sense that it calls variants based on the literal sequences of reads aligned to a particular target, not their precise alignment. This model is a straightforward generalization of previous ones (e.g. PolyBayes, samtools, GATK) which detect or report variants based on alignments. This method avoids one of the core problems with alignment-based variant detection — that identical sequences may have multiple possible alignments:” | ||
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| ## Usage | ||
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| Basic usage: | ||
| ``` | ||
| freebayes -f [REFERENCE] [OPTIONS] [BAM FILES] >[OUTPUT] | ||
| ``` | ||
| Example usage: | ||
| ``` | ||
| freebayes --bam Sample_1_sorted.bam --ploidy 1 --fasta-reference reference.fasta --vcf Sample1_freebayes.vcf | ||
| ``` | ||
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| There are LOTS of options so use `freebayes --help` to get full list. |