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man page of bcftools

bcftools: Utilities for the Binary Call Format (BCF) and VCF.


bcftools - Utilities for the Binary Call Format (BCF) and VCF.


bcftools index in.bcf bcftools view in.bcf chr2:100-200 > out.vcf bcftools view -vc in.bcf > out.vcf 2> out.afs


Bcftools is a toolkit for processing VCF/BCF files, calling variants and estimating site allele frequencies and allele frequency spectrums.
view bcftools view [-AbFGNQSucgv] [-D seqDict] [-l listLoci] [-s listSample] [-i gapSNPratio] [-t mutRate] [-p varThres] [-P prior] [-1 nGroup1] [-d minFrac] [-U nPerm] [-X permThres] in.bcf [region] Convert between BCF and VCF, call variant candidates and estimate allele frequencies. Input/Output Options: -A Retain all possible alternate alleles at variant sites. By default, the view command discards unlikely alleles. -b Output in the BCF format. The default is VCF. -D FILE Sequence dictionary (list of chromosome names) for VCF->BCF conversion [null] -F Indicate PL is generated by r921 or before (ordering is different). -G Suppress all individual genotype information. -l FILE List of sites at which information are outputted [all sites] -N Skip sites where the REF field is not A/C/G/T -Q Output the QCALL likelihood format -s FILE List of samples to use. The first column in the input gives the sample names and the second gives the ploidy, which can only be 1 or 2. When the 2nd column is absent, the sample ploidy is assumed to be 2. In the output, the ordering of samples will be identical to the one in FILE. [null] -S The input is VCF instead of BCF. -u Uncompressed BCF output (force -b). Consensus/Variant Calling Options: -c Call variants using Bayesian inference. This option automatically invokes option -e. -d FLOAT When -v is in use, skip loci where the fraction of samples covered by reads is below FLOAT. [0] -e Perform max-likelihood inference only, including estimating the site allele frequency, testing Hardy-Weinberg equlibrium and testing associations with LRT. -g Call per-sample genotypes at variant sites (force -c) -i FLOAT Ratio of INDEL-to-SNP mutation rate [0.15] -p FLOAT A site is considered to be a variant if P(ref|D)<FLOAT [0.5] -P STR Prior or initial allele frequency spectrum. If STR can be full, cond2, flat or the file consisting of error output from a previous variant calling run. -t FLOAT Scaled muttion rate for variant calling [0.001] -v Output variant sites only (force -c) Contrast Calling and Association Test Options: -1 INT Number of group-1 samples. This option is used for dividing the samples into two groups for contrast SNP calling or association test. When this option is in use, the following VCF INFO will be outputted: PC2, PCHI2 and QCHI2. [0] -U INT Number of permutations for association test (effective only with -1) [0] -X FLOAT Only perform permutations for P(chi^2)<FLOAT (effective only with -U) [0.01] index bcftools index in.bcf Index sorted BCF for random access. cat bcftools cat in1.bcf [in2.bcf [...]]] Concatenate BCF files. The input files are required to be sorted and have identical samples appearing in the same order.
+------+-----------+--------------------------------------------------------------------------------------+ | Tag | Format | Description | +------+-----------+--------------------------------------------------------------------------------------+ |AF1 | double | Max-likelihood estimate of the site allele frequency (AF) of the first ALT allele | |CI95 | double[2] | Equal-tail Bayesian credible interval of AF at the 95% level | |DP | int | Raw read depth (without quality filtering) | |DP4 | int[4] | # high-quality reference forward bases, ref reverse, alternate for and alt rev bases | |FQ | int | Consensus quality. Positive: sample genotypes different; negative: otherwise | |MQ | int | Root-Mean-Square mapping quality of covering reads | |PC2 | int[2] | Phred probability of AF in group1 samples being larger (,smaller) than in group2 | |PCHI2 | double | Posterior weighted chi^2 P-value between group1 and group2 samples | |PV4 | double[4] | P-value for strand bias, baseQ bias, mapQ bias and tail distance bias | |QCHI2 | int | Phred-scaled PCHI2 | |RP | int | # permutations yielding a smaller PCHI2 | +------+-----------+--------------------------------------------------------------------------------------+ BCFTOOLS(1)

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