Mercurial > repos > siyuan > prada
diff pyPRADA_1.2/tools/samtools-0.1.16/bcftools/bcftools.1 @ 0:acc2ca1a3ba4
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author | siyuan |
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date | Thu, 20 Feb 2014 00:44:58 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pyPRADA_1.2/tools/samtools-0.1.16/bcftools/bcftools.1 Thu Feb 20 00:44:58 2014 -0500 @@ -0,0 +1,189 @@ +.TH bcftools 1 "16 March 2011" "bcftools" "Bioinformatics tools" +.SH NAME +.PP +bcftools - Utilities for the Binary Call Format (BCF) and VCF. +.SH SYNOPSIS +.PP +bcftools index in.bcf +.PP +bcftools view in.bcf chr2:100-200 > out.vcf +.PP +bcftools view -vc in.bcf > out.vcf 2> out.afs + +.SH DESCRIPTION +.PP +Bcftools is a toolkit for processing VCF/BCF files, calling variants and +estimating site allele frequencies and allele frequency spectrums. + +.SH COMMANDS AND OPTIONS + +.TP 10 +.B view +.B bcftools view +.RB [ \-AbFGNQSucgv ] +.RB [ \-D +.IR seqDict ] +.RB [ \-l +.IR listLoci ] +.RB [ \-s +.IR listSample ] +.RB [ \-i +.IR gapSNPratio ] +.RB [ \-t +.IR mutRate ] +.RB [ \-p +.IR varThres ] +.RB [ \-P +.IR prior ] +.RB [ \-1 +.IR nGroup1 ] +.RB [ \-d +.IR minFrac ] +.RB [ \-U +.IR nPerm ] +.RB [ \-X +.IR permThres ] +.I in.bcf +.RI [ region ] + +Convert between BCF and VCF, call variant candidates and estimate allele +frequencies. + +.RS +.TP +.B Input/Output Options: +.TP 10 +.B -A +Retain all possible alternate alleles at variant sites. By default, the view +command discards unlikely alleles. +.TP 10 +.B -b +Output in the BCF format. The default is VCF. +.TP +.BI -D \ FILE +Sequence dictionary (list of chromosome names) for VCF->BCF conversion [null] +.TP +.B -F +Indicate PL is generated by r921 or before (ordering is different). +.TP +.B -G +Suppress all individual genotype information. +.TP +.BI -l \ FILE +List of sites at which information are outputted [all sites] +.TP +.B -N +Skip sites where the REF field is not A/C/G/T +.TP +.B -Q +Output the QCALL likelihood format +.TP +.BI -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 +.IR FILE . +[null] +.TP +.B -S +The input is VCF instead of BCF. +.TP +.B -u +Uncompressed BCF output (force -b). +.TP +.B Consensus/Variant Calling Options: +.TP 10 +.B -c +Call variants using Bayesian inference. This option automatically invokes option +.BR -e . +.TP +.BI -d \ FLOAT +When +.B -v +is in use, skip loci where the fraction of samples covered by reads is below FLOAT. [0] +.TP +.B -e +Perform max-likelihood inference only, including estimating the site allele frequency, +testing Hardy-Weinberg equlibrium and testing associations with LRT. +.TP +.B -g +Call per-sample genotypes at variant sites (force -c) +.TP +.BI -i \ FLOAT +Ratio of INDEL-to-SNP mutation rate [0.15] +.TP +.BI -p \ FLOAT +A site is considered to be a variant if P(ref|D)<FLOAT [0.5] +.TP +.BI -P \ STR +Prior or initial allele frequency spectrum. If STR can be +.IR full , +.IR cond2 , +.I flat +or the file consisting of error output from a previous variant calling +run. +.TP +.BI -t \ FLOAT +Scaled muttion rate for variant calling [0.001] +.TP +.B -v +Output variant sites only (force -c) +.TP +.B Contrast Calling and Association Test Options: +.TP +.BI -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] +.TP +.BI -U \ INT +Number of permutations for association test (effective only with +.BR -1 ) +[0] +.TP +.BI -X \ FLOAT +Only perform permutations for P(chi^2)<FLOAT (effective only with +.BR -U ) +[0.01] +.RE + +.TP +.B index +.B bcftools index +.I in.bcf + +Index sorted BCF for random access. +.RE + +.TP +.B cat +.B bcftools cat +.I in1.bcf +.RI [ "in2.bcf " [ ... "]]]" + +Concatenate BCF files. The input files are required to be sorted and +have identical samples appearing in the same order. +.RE + +.SH BCFTOOLS SPECIFIC VCF TAGS + +.TS +center box; +cb | cb | cb +l | l | l . +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 +.TE