Initial directory structure.

git-svn-id: https://xspecies-exome.googlecode.com/svn/trunk@1 2a9ec0da-e0e1-8bab-d9b4-ab8d0290936b
Added test data

git-svn-id: https://xspecies-exome.googlecode.com/svn/trunk@2 2a9ec0da-e0e1-8bab-d9b4-ab8d0290936b
Changed directory structure

git-svn-id: https://xspecies-exome.googlecode.com/svn/trunk@3 2a9ec0da-e0e1-8bab-d9b4-ab8d0290936b
Starting to build pipeline that aligns with BWA

git-svn-id: https://xspecies-exome.googlecode.com/svn/trunk@4 2a9ec0da-e0e1-8bab-d9b4-ab8d0290936b
Pipeline largely complete from alignment through final BAM

git-svn-id: https://xspecies-exome.googlecode.com/svn/trunk@5 2a9ec0da-e0e1-8bab-d9b4-ab8d0290936b
Added flagstat and idxstats to end of alignment pipeline

git-svn-id: https://xspecies-exome.googlecode.com/svn/trunk@6 2a9ec0da-e0e1-8bab-d9b4-ab8d0290936b
Roughly outlined rest of makefile

git-svn-id: https://xspecies-exome.googlecode.com/svn/trunk@7 2a9ec0da-e0e1-8bab-d9b4-ab8d0290936b
Outlined steps for post-alignment filtering

git-svn-id: https://xspecies-exome.googlecode.com/svn/trunk@8 2a9ec0da-e0e1-8bab-d9b4-ab8d0290936b
Added individual ID to filenames

git-svn-id: https://xspecies-exome.googlecode.com/svn/trunk@9 2a9ec0da-e0e1-8bab-d9b4-ab8d0290936b
Fixed a few bugs in alignment steps relating to variable export

git-svn-id: https://xspecies-exome.googlecode.com/svn/trunk@10 2a9ec0da-e0e1-8bab-d9b4-ab8d0290936b
Updated paper outline

git-svn-id: https://xspecies-exome.googlecode.com/svn/trunk@12 2a9ec0da-e0e1-8bab-d9b4-ab8d0290936b
Added FastQC analysis of raw reads

git-svn-id: https://xspecies-exome.googlecode.com/svn/trunk@13 2a9ec0da-e0e1-8bab-d9b4-ab8d0290936b
Added pre-alignment filtering with FastX

git-svn-id: https://xspecies-exome.googlecode.com/svn/trunk@14 2a9ec0da-e0e1-8bab-d9b4-ab8d0290936b
Forgot to add script

git-svn-id: https://xspecies-exome.googlecode.com/svn/trunk@15 2a9ec0da-e0e1-8bab-d9b4-ab8d0290936b
Added post-alignment steps: fix mate pairs and filter for those mapped and paired correctly

git-svn-id: https://xspecies-exome.googlecode.com/svn/trunk@16 2a9ec0da-e0e1-8bab-d9b4-ab8d0290936b
Added bamtools stats to post-alignment analysis

git-svn-id: https://xspecies-exome.googlecode.com/svn/trunk@17 2a9ec0da-e0e1-8bab-d9b4-ab8d0290936b
Added post-alignment step: remove duplicates

git-svn-id: https://xspecies-exome.googlecode.com/svn/trunk@18 2a9ec0da-e0e1-8bab-d9b4-ab8d0290936b
Finished post-alignment filtering steps. Also, added scripts that I had forgotten for post-alignment filtering steps

git-svn-id: https://xspecies-exome.googlecode.com/svn/trunk@19 2a9ec0da-e0e1-8bab-d9b4-ab8d0290936b
Split sort and index. Indexed mapped reads that passed.

git-svn-id: https://xspecies-exome.googlecode.com/svn/trunk@20 2a9ec0da-e0e1-8bab-d9b4-ab8d0290936b
Updated paper outline

git-svn-id: https://xspecies-exome.googlecode.com/svn/trunk@21 2a9ec0da-e0e1-8bab-d9b4-ab8d0290936b