A simple perl script that converts files in the .genious format to fasta format.
Runs with the following command:
genious_to_fasta.pl -i
#vcf2hp2.pl
Reformats vcf file as hapmap file. Has a few RILAB specific options hard-coded. Written by Jer-Ming Chia.
Usage: SFS.pl -F
the argument accepts the wildcard * character for multiple files
Optional command line arguments:
-q removes header (only if -f is not also chosen)
-n new sample size
-f prints out frequency counts of derived mutations at every site
--condition conditions on observing a site as polymorphic in the new sample size
--unrounded returns unrounded frequencies
--folded calculates folded SFS
--version prints version and license information
Required command line parameters:
-I 'filename' : input name of fasta file(s) (accepts * wildcard).
Optional command line parameters:
-V : for verbose output
-N : turn end gaps into N's
-M : turn all characters except A,C,G,T,_ into N's
-O : outputs to file 'filename'.out instead of stdout
-C : changelog since version 1.0
-S : splits alignment into separate files for groups of sequence ID's
-G : replaces Genbank ID's with species name (requires Bioperl installation)
The default format from GENOME STUDIO looks something like:
[Header] GSGT Version 1.1.9 Processing Date 5/3/2011 10:10 AM Content MaizeSNP50_A.bpm Num SNPs 55126 Total SNPs 56110 Num Samples 94 Total Samples 94 [Data] RIMMA0662.1 RIMMA0665.1 RIMMA0394.2 RIMMA0404.1 abph1.15 GG GG AA AA abph1.22 AA AA AA AA
ktohap version 1.0 can be run as follows:
ktohap.pl -i <INFILE> -o <OUTFILE> <OPTIONS>
Where <INFILE> is a file in the default Genome Studio output format
and <OUTFILE> is the base name of the hapmap-formatted output file.
Also requires a file called “snpdata.txt” that has information on SNP locations and types, in the following format:
PZE0000200501 0 4894262 hapmap
PZE0000344524 0 4921654 hapmap
PZE0008211605 0 2572930 hapmap
Where first column is SNP name, then chromosome, then position on chromosome, then SNP type.
Optional flags include:
-f <FORMAT> Currently only accepts teh default \"hapmap\" but other formats may be available soon
-d Makes ktohap report both alleles instead of treating heterozygotes as ambiguity codes.
--inst <NAME> Defines institution column. Default is UCD
--panel <NAME> Defines panel column. Default is \"NA\";
HapToTab version 2.1 can be run as follows:
HapToTab.pl <INFILE> <--snp or --bp> <INT> <OPTIONS>
Where <INFILE> is a file in hapmap format.
HapToTab needs to know the window size either in SNPs or bp (e.g. --snp 100 or --bp 10000).
A negative number for SNPs will run HapToTab using only one window for the whole file.
The following options are available:
--g <NAME> name the group you are running haptotab on. default is \"all\"
--maxdip format the output files for Hudson's maxdip program
--maxhap format the output files for Hudson's maxhap program
--nohets remove all heterozygotes (code as missing data)
--out file has an outgroup (assumes the last column in the hapmap file)
--freq <INT> filters out all SNPs with a frequency less than INT in the data\n\n";
Code samples sequences randomly from a fastq file.
Run as samperl.pl
#subcode.pl Barcode subthingy version 1.0
Usage: perl subcode.pl
-i
-n
-j <optional file of barcodes you want included
Barcode file format should be \t on each line. Assumes you have a list of 96 or more potential barcodes.