bcftools plugin -lv
-- GTisec --
Count genotype intersections across all possible sample subsets in a vcf file.
-- GTsubset --
Output only sites where the requested samples all exclusively share a genotype (GT).
-- ad-bias --
Find positions with wildly varying ALT allele frequency (Fisher test on FMT/AD).
-- add-variantkey --
Add VariantKey INFO fields VKX and RSX.
-- af-dist --
AF and GT probability distribution stats.
-- allele-length --
Count the frequency of the length of REF, ALT and REF+ALT
-- check-ploidy --
Check if ploidy of samples is consistent for all sites
-- check-sparsity --
Print samples without genotypes in a region or chromosome
-- color-chrs --
Color shared chromosomal segments, requires phased GTs.
-- contrast --
Find novel alleles and genotypes in two groups of samples.
-- counts --
A minimal plugin which counts number of samples, SNPs,
INDELs, MNPs and total number of sites.
-- dosage --
Prints genotype dosage determined from tags requested by the user.
-- fill-AN-AC --
Fill INFO fields AN and AC. This plugin is DEPRECATED, use fill-tags instead.
-- fill-from-fasta --
Fill INFO or REF field based on values in a fasta file
-- fill-tags --
Set INFO tags AF, AC, AC_Hemi, AC_Hom, AC_Het, AN, ExcHet, HWE, MAF, NS; FORMAT/VAF and more.
-- fixploidy --
Fix ploidy.
-- fixref --
Fix reference strand orientation, e.g. from Illumina/TOP to fwd.
-- frameshifts --
Annotate frameshift indels.
-- guess-ploidy --
Determine sample sex by checking genotype likelihoods in haploid regions.
-- gvcfz --
Compress gVCF file by resizing gVCF blocks according to specified criteria.
-- impute-info --
Add imputation information metrics to the INFO field based on selected FORMAT tags.
-- indel-stats --
Calculate indel stats scanning over a range of thresholds simultaneously.
-- isecGT --
Compare two files and set non-identical genotypes to missing.
-- mendelian2 --
Count Mendelian consistent / inconsistent genotypes.
-- missing2ref --
Set missing genotypes ("./.") to ref or major allele ("0/0" or "0|0").
-- parental-origin --
Determine parental origin of a CNV region in a trio.
-- prune --
Annotate sites with or prune sites by linkage disequilibrium or number of sites within a window
-- remove-overlaps --
Remove, list or mark overlapping variants
-- scatter --
Scatter VCF by chunks or regions, creating multiple VCFs.
-- setGT --
Set genotypes: partially missing to missing, missing to ref/major allele, etc.
-- smpl-stats --
Calculate basic per-sample stats scanning over a range of thresholds simultaneously.
-- split --
Split VCF by sample, creating single- or multi-sample VCFs
-- split-vep --
Query structured annotations such as INFO/CSQ produced by VEP of INFO/BCSQ produced by bctools/csq.
-- tag2tag --
Convert between similar tags, such as GL,PL,GP or QR,QA,QS or localized alleles, eg PL,LPL.
-- trio-dnm2 --
Screen variants for possible de-novo mutations in trios.
-- trio-stats --
Calculate transmission rate and other stats in trio children.
-- trio-switch-rate --
Calculate phase switch rate in trio samples, children samples must have phased GTs.
-- variant-distance --
Annotate sites with distance to the nearest variant
-- variantkey-hex --
Generate VariantKey index files
-- vcf2table --
Convert VCF to tables in the terminal.
Author Pierre Lindenbaum PhD. Institut-du-Thorax. U1087. Nantes/France
Options:
-h|--help (string) help (this screen).
-x|--hide (string) comma separated list of features to hide:
HOM_REF or RR : genotypes with REF allele only
HET or AR : heterozygous genotypes
NO_CALL or MISSING : missing genotypes
CSQ or VEP : VEP table
SPLICEAI : SPLICEAI table
ANN or SNPEFF : SNPEFF table
LOF: SNPEFF LOF table
VC: general table
INFO: INFO table
GT: Genotype table
GTTYPES: Genotype count table
URL: hyperlink table
Example:
$ wget -O - 'http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/ALL.chr22.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz' |\
bcftools +vcf2table -i 'AC<10' -- --hide 'HOM_REF,INFO,NO_CALL'
(...)
<<< 22:10714247:C (n. 446)
+--------+----------+
| KEY | VALUE |
+--------+----------+
| CHROM | 22 |
| POS | 10714247 |
| ID | . |
| REF | C |
| ALT | G |
| QUAL | . |
| FILTER | PASS |
+--------+----------+
+-----------+-------+----------+
| Type | Count | % |
+-----------+-------+----------+
| REF only | 2545 | 99.8823 |
| HET | 3 | 0.117739 |
+-----------+-------+----------+
+---------+-------+-----+
| SAMPLE | GTYPE | GT |
+---------+-------+-----+
| HG03136 | HET | 1|0 |
| HG03171 | HET | 0|1 |
| HG03270 | HET | 0|1 |
+---------+-------+-----+
>>> 22:10714247:C (n. 446)
-- vrfs --
Localised assessment of sequencing artefacts, estimate site noisiness (variant read frequency score)
