moe's data, remove duplicates

Post date: Aug 27, 2014 2:39:44 PM

I used samtools to remove PCR duplicates. For some reason there appear to be only 1507 sorted bam files, rather than 1536 as I suspected. I need to check the logs.

Here is the code:

cd /home/A01963476/data/timema/moe_radiation_wgrs/alignments/

samtools rmdup aln_WTCHG_135840_296.sorted.bam aln_WTCHG_135840_296_unique.bam

samtools index aln_WTCHG_135840_296_unique.bam