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
- -e, --erase-empty-columns
-
Remove columns with no characters (all gaps).
- --minor-allele arg
-
Keep columns with minor-allele count >= arg
- --missing-freq arg (=1)
-
Keep columns with missing frequency >= arg
- --one-every arg
-
Keep only 1 column in each interval of size arg
- -G arg, --mask-gaps
arg
-
Remove columns within arg columns of a gap
- -S, --strip-gaps
-
Remove columns within arg columns of a gap
- --gap-fraction arg (=0.01)
-
Fraction of sequences that need to have a gap
- -M arg, --mask-file
arg
-
Apply mask-file
- -A, --autoclean
-
Mask blocks with too many SNPs
- --dical2
-
Output file for DiCal2
- --msmc
-
Output file for MSMC
- --psmc
-
Output file for PSMC
- --write-bed arg
-
Output BED file with chromosome name arg
- --variant arg (=1)
-
Is there a SNP at distance arg from SNP?
- --consensus-seqs arg
-
sequences to use in consensus
- --translate-mask arg
-
Masks (CSV or @file)
- --translate-vcf arg
-
Masks (CSV or @file)
- --show-freq
-
Show allele frequencies
- --clean-to-ref arg
-
Remove columns not in reference sequence arg
- --pi-matrix
-
Calculate pi for each pair of sequences
- --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
- -m arg, --mask-alleles
arg
-
Find alleles with S snps in L bases and count >= N
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.