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Gist 39d6a8d17d83eb8f17c0926e30809957

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Last edited Feb 8, 2019
Created on Feb 8, 2019

This example shows a variant-filtering pipeline for genomic data, using bcftools to process VCF files from two different callers (samtools mpileup and freebayes). The script applies quality and proximity filters, including minimum QUAL scores, distance to indels, and indel cluster thresholds, via the bcftools filter command with options like `-i'%QUAL>10'`, `-g3`, and `-G10`. The output writes filtered VCF files with a LOWQUAL annotation for variants that fail the criteria. The code relies on the bcftools command-line API rather than a visualization library, and the data source is the initial VCF files in the variants directory.

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Gist ac0e4a9bdb2f03d365c4402d04ecba09

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Gist 9a3defa4596db38a11fc0ec9549b4834

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Gist b503b3f905281f7da44c76ba5ed1d8d9

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Gist d5a955d9a667be4ff4afe7064affbb31

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Gist aa8c974207019f98e6d45a49488b2c4b

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