setup bam headers and check


Former-commit-id: 3cdd57dfdce69ff71b289570931241b12f20dda9
working on 235 --> 220/ce10 liftover script


Former-commit-id: 51aff332bc2cddc068ccfa11b67a045fbc062dc3
Part 1 of leftover script almost done. Getting tripped up on relative vs. abs. dirs! ARRRRGH


Former-commit-id: 84eb7479700858b128a945a30ddb0a24e067da4a
First part of leftover process appears to be 'working'; many aspects of this could be accomplished much easier in python. Something to consider possibly...?


Former-commit-id: 7f88d70d3684dba671fcd79db4356b2e27022366
Alternative leftover strategy devised


Former-commit-id: 5af1c9907f44502109ea65f46bd35d86f5ed6bf8
ignore .gff, vcf


Former-commit-id: 95e22e012804456004f489188984c40be1719266
ignore mmp data


Former-commit-id: 1ee09b1e4488d0946c6b43d881298a465cac0733
Updating bam retrieval.


Former-commit-id: 11834f058f44c172a905a152f7bd1e48f8f22b3b
BGI2 naming issues resolved


Former-commit-id: dffaf367d1546c4d535828de118e90ed38a6f0a5
BGI2 naming issues resolved (2)


Former-commit-id: e55a203ff42358c51c13d6e6ba12afc3a7cf7f85
Merge branch 'master' of https://github.com/AndersenLab/Variant-Caller-Pipeline

Conflicts:
	.gitignore

Former-commit-id: b18a136467a9a6c8b1d99d931cb2823ad1161c47
adding cluster scripts


Former-commit-id: 2dba10fdd8753dcaaa9822df9bfa71fca8bcf91c
ignore sam files


Former-commit-id: 7a1d0c6443b696de8a1a19d35b8f8212d6a51492
Ignore fq.gz


Former-commit-id: 77a1972675cf9ef9f556b2449d6f2fa52bd78dc1
ignore .bam.zip


Former-commit-id: 134d82f6a1fe3e4622ffa2ffbd9ab753e7902b4c
git ignore messed up


Former-commit-id: 54082e1d831f74022ffc1a9135b6c0d680f01de6
fix


Former-commit-id: e2b467999f40c8fa268c7ff4173a2be85e5e47d5
Add manifest and strain accounting


Former-commit-id: 31f2ab42bfaf2025bc5911ba82a8db23506dd5ca
Delete select files from manifest


Former-commit-id: 20ff5c6d3fe083ef074c63bd808484317eb6d06e
filenames added


Former-commit-id: 525fab3997d556661983bba4edab3a009836b2ec