X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bcftools%2Fbcftools.1;fp=bcftools%2Fbcftools.1;h=0000000000000000000000000000000000000000;hp=c6b496867340207585ff6e3a6befa5cf72262c6b;hb=e2bd290b8643f0a728c282a8b825392307750210;hpb=9f4bebab2e0917c676ae739b2d05cb22ad6c4ed5 diff --git a/bcftools/bcftools.1 b/bcftools/bcftools.1 deleted file mode 100644 index c6b4968..0000000 --- a/bcftools/bcftools.1 +++ /dev/null @@ -1,189 +0,0 @@ -.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)