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42 lines
1.6 KiB
Plaintext
42 lines
1.6 KiB
Plaintext
---
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syntax: markdown
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tags: [tldr, common]
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source: https://github.com/tldr-pages/tldr.git
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---
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# bcftools
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> Tools for manipulating VCF and BCF files.
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> More information: <https://samtools.github.io/bcftools/bcftools.html>.
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- View BCF file and convert to [v]CF on `stdout`:
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`bcftools view {{path/to/input.bcf}} {{[-O|--output-type]}} v`
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- Sort a VCF file variants by chromosome and position, output to a [b]CF file, and index the sorted output:
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`bcftools sort {{path/to/input.vcf.gz}} {{[-O|--output-type]}} b {{[-o|--output]}} {{path/to/sorted.bcf}} {{[-W|--write-index]}}`
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- Concatenate sorted VCF files that share the same samples to [z]ipped VCF on `stdout`:
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`bcftools concat {{path/to/chr1.vcf.gz path/to/chr2.vcf.gz ...}} {{[-O|--output-type]}} z`
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- Filter for low quality variants and annotate with "LowQual" tag in the FILTER column:
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`bcftools filter {{[-e|--exclude]}} 'QUAL<20' {{[-s|--soft-filter]}} LowQual {{path/to/input.vcf.gz}}`
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- Add annotated columns from a tabix-indexed table on `stdout`:
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`bcftools annotate {{[-a|--annotations]}} {{path/to/annotations.tsv.gz}} {{[-c|--columns]}} CHROM,POS,REF,ALT,INFO/AF {{path/to/input.vcf.gz}}`
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- Output variant [i]nter[sec]tion between VCF files using 4 threads:
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`bcftools isec {{path/to/a.vcf.gz path/to/b.vcf.gz ...}} --threads 4 {{[-o|--output]}} {{path/to/intersection.vcf}}`
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- Merge non-overlapping samples from VCF files without indices on `stdout`:
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`bcftools merge {{path/to/cohort1.vcf.gz}} {{path/to/cohort2.vcf.gz}} --no-index`
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- Create index for a bgzipped VCF file:
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`bcftools index {{path/to/input.vcf.gz}}`
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