X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sam%2Fbcftools%2Fbcftools.1;fp=sam%2Fbcftools%2Fbcftools.1;h=0000000000000000000000000000000000000000;hb=946f9a6adb2a82048c8453d44693cd3838d32939;hp=6c7403bea6b8b6ebde3c77a8a1ef55ee890fcd59;hpb=9712cd844059fd5cd25b52162ae10bc1d756d899;p=rsem.git diff --git a/sam/bcftools/bcftools.1 b/sam/bcftools/bcftools.1 deleted file mode 100644 index 6c7403b..0000000 --- a/sam/bcftools/bcftools.1 +++ /dev/null @@ -1,120 +0,0 @@ -.TH bcftools 1 "2 October 2010" "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 [ \-cbuSAGgHvNQ ] -.RB [ \-1 -.IR nGroup1 ] -.RB [ \-l -.IR listFile ] -.RB [ \-t -.IR mutRate ] -.RB [ \-p -.IR varThres ] -.RB [ \-P -.IR prior ] -.I in.bcf -.RI [ region ] - -Convert between BCF and VCF, call variant candidates and estimate allele -frequencies. - -.B OPTIONS: -.RS -.TP 10 -.B -b -Output in the BCF format. The default is VCF. -.TP -.B -c -Call variants. -.TP -.B -v -Output variant sites only (force -c) -.TP -.B -g -Call per-sample genotypes at variant sites (force -c) -.TP -.B -u -Uncompressed BCF output (force -b). -.TP -.B -S -The input is VCF instead of BCF. -.TP -.B -A -Retain all possible alternate alleles at variant sites. By default, this -command discards unlikely alleles. -.TP -.B -G -Suppress all individual genotype information. -.TP -.B -H -Perform Hardy-Weiberg Equilibrium test. This will add computation time, sometimes considerably. -.TP -.B -N -Skip sites where the REF field is not A/C/G/T -.TP -.B -Q -Output the QCALL likelihood format -.TP -.B -f -Reference-free variant calling mode. In this mode, the prior will be -folded; a variant is called iff the sample(s) contains at least two -alleles; the QUAL field in the VCF/BCF output is changed accordingly. -.TP -.BI "-1 " INT -Number of group-1 samples. This option is used for dividing input into -two groups for comparing. A zero value disables this functionality. [0] -.TP -.BI "-l " FILE -List of sites at which information are outputted [all sites] -.TP -.BI "-t " FLOAT -Scaled muttion rate for variant calling [0.001] -.TP -.BI "-p " FLOAT -A site is considered to be a variant if P(ref|D)