SNP calling using samtools

edit bash file
$open .bash_profile

copy file to server share folder
$rsync -avz "filename" chinstrap:/store/share/Andes

1. download sequence data (in .sra form)
2. convert .sra to .fastq using sratoool kit
$ fastq-dump --split-files SRR11511287

$ /Users/andesli/Desktop/sratoolkit.2.5.0-1-mac64/bin/fastq-dump SRR1151287 (download)

$ /Users/andesli/Desktop/sratoolkit.2.5.0-1-mac64/bin/fastq-dump -A /Users/andesli/Desktop/bifido_seq_data/test/hi_seq_breve_jcm1192/SRR1151287.sra (convert)

flow diagram:

step1 : Align

(follow link http://ged.msu.edu/angus/tutorials-2011/bwa_tutorial.html)