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bio-variant-calling

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Call SNPs and indels from aligned reads using bcftools mpileup and call. Use when detecting variants from BAM files or generating VCF from alignments.

When to use

• Detecting SNPs and indels
• Generating VCF from alignments
• Variant calling from BAM files
• Multi-sample variant calling
• Calling specific regions
• Parallel variant calling by chromosome

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Source