Update cheatsheets

tldr/bcftools

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