User:Lindenb/Notebook/UMR915/20110202
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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. <html><script src="https://gist.github.com/807481.js?file=bamsorted.c"></script></html>
