alignment-smc(1)

NAME

alignment-smc - Generate input for SMC programs.

SYNOPSIS

alignment-smc alignment-file [OPTIONS]

DESCRIPTION

Generate input for SMC programs.

ALLOWED OPTIONS:

-h, --help
    produce help message

--align arg
    file with sequences and initial alignment

--alphabet arg
    specify the alphabet: DNA, RNA, Amino-Acids, Triplets, or Codons

-S, --strip-gaps
    Remove columns within arg columns of a gap

-G arg, --mask-gaps arg
    Remove columns within arg columns of a gap

-M arg, --mask-file arg
    Apply mask-file

--minor-allele arg
    Keep columns with given minor-allele count

--one-every arg
    Keep only 1 column in each interval of size arg

--write-bed arg
    Write selected columns in BED format with chromosome name arg

--show-freq
    Show allele frequencies

--translate-mask arg
    Masks (CSV or @file)

--translate-vcf arg
    Masks (CSV or @file)

--variant arg (=1)
    Is there a SNP at distance arg from SNP?

--dical2
    Output file for DiCal2

--clean-to-ref arg
    Remove columns not in reference sequence arg

--msmc
    Output file for MSMC

--psmc
    Output file for PSMC

--pi-matrix
    Calculate pi for each pair of sequences

--autoclean
    Mask blocks with too many SNPs

--histogram arg
    Output SNP counts for blocks of arg bases

--snp-snp-lengths arg
    Output counts of snp-snp lengths up to arg snps

--sfs2d arg
    pop1:pop2:anc:window

--find-alleles arg
    Find alleles with S snps in L bases and count >= N

--consensus-seqs arg
    sequences to use in consensus

EXAMPLES:

To calculate some statistics:

    % alignment-smc sequence.fasta > /dev/null

To write out SNPS with minor-allele count >=2 in BED format:

    % alignment-smc sequences.fasta --minor-allele=2 --write-bed=chrom > snps.bed

REPORTING BUGS:

BAli-Phy online help: <http://www.bali-phy.org/docs.php>.

Please send bug reports to <bali-phy-users@googlegroups.com>.

AUTHORS
Benjamin Redelings.