User:Lindenb/Notebook/UMR915/20110202

=Proteomics= Added some features for Céline's program =Project 'B'=
 * end of markdup, now indexing and running the GATK for CountCovariates. I wanted to use --DBSNP=(...)/dbsnp_130_b36.rod but there is no "chr" prefix for the chromosome. So I created sed 's/\t/\tchr/' dbsnp_130_b36.rod > dbsnp_130_hg18.rod

wrote a tool to test whether a BAM file is sorted: https://gist.github.com/807481. Asked for help on the samtools mailing list to improve the code. 