Download Latest Version NA12878_Calls.tar.gz (2.0 MB)
Email in envelope

Get an email when there's a new version of STRYPE

Home
Name Modified Size InfoDownloads / Week
NA12878_Calls.tar.gz 2011-07-18 2.0 MB
0
STRYPE_v0.03.tar.gz 2011-06-09 11.4 MB
0
README 2011-03-29 911 Bytes
0
STRYPE_v0.02.tar.gz 2011-03-29 11.4 MB
0
STRYPE_v0.01.tar.gz 2011-03-28 11.4 MB
0
STRYPE.tar.gz 2011-03-24 11.4 MB
0
Totals: 6 Items   47.7 MB 0 
In order to run STRYPE, you will need a recent version of SAMTOOLS (http://samtools.sourceforge.net/) 
installed on your computer as well as PERL. 

To run STRYPE out of the box, you will first need to download an example BAM file from ftp://ftp.sanger.ac.uk/pub/1000genomes/ww4/
which is from sequenced individual NA18507 (Bentley, 2008).  Next, run STRYPE with the following command:

./STRYPE.pl <file.bam> <mer> <positions> <chr> <prior> <lib_distributions>

Example command for chromosome 20 run:

./STRYPE.pl NA18507_chr20.bam 3 3mers 20 indel_priors_all_symmetric_3mers.txt Lib_Distributions_NA18507

This will generate a list of genotype calls in the file VariantCalls/Chromosome20/Results.txt .

The output in the Results.txt file is as follows:

<chr> <mer> <repeat_start_pos> <repeat_end_pos> <repeat_len> <allele1> <allele2> <max_posterior> <ref_posterior> <num_spanning_reads> <norm_test> <ratio>
Source: README, updated 2011-03-29