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Merge pull request #1032 from Kincekara/master
update readmes for bcftools, htslib, and samtools
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# bcftools container | ||
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Main tool: | ||
Main tool: [bcftools](https://github.com/samtools/bcftools) | ||
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* [bcftools](https://github.com/samtools/bcftools) | ||
Code repository: https://github.com/samtools/bcftools | ||
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Basic information on how to use this tool: | ||
- executable: bcftools | ||
- help: --help | ||
- version: --version | ||
- description: BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF. | ||
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Additional information: | ||
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This container includes bcftools v1.20 compiled with **libdeflate** for a better cloud performance. Also, "polysomy" and plugins are enabled in this image. | ||
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Full documentation: https://samtools.github.io/bcftools/howtos/index.html | ||
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## Example Usage | ||
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```bash | ||
bcftools mpileup -A -d 200 -B -Q 0 -f {reference_genome} {bam} | bcftools call -mv -Ov -o bcftools_variants/{sample}.vcf | ||
``` | ||
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Better documentation can be found at [https://www.htslib.org/doc/bcftools.html](https://www.htslib.org/doc/bcftools.html) | ||
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