Name | Modified | Size | Downloads / Week |
---|---|---|---|
NA12878_Calls.tar.gz | 2011-07-18 | 2.0 MB | |
STRYPE_v0.03.tar.gz | 2011-06-09 | 11.4 MB | |
README | 2011-03-29 | 911 Bytes | |
STRYPE_v0.02.tar.gz | 2011-03-29 | 11.4 MB | |
STRYPE_v0.01.tar.gz | 2011-03-28 | 11.4 MB | |
STRYPE.tar.gz | 2011-03-24 | 11.4 MB | |
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>