setup bam headers and check
working on 235 --> 220/ce10 liftover script
Part 1 of leftover script almost done. Getting tripped up on relative vs. abs. dirs! ARRRRGH
First part of leftover process appears to be 'working'; many aspects of this could be accomplished much easier in python. Something to consider possibly...?
Alternative leftover strategy devised
ignore .gff, vcf
ignore mmp data
Updating bam retrieval.
BGI2 naming issues resolved
BGI2 naming issues resolved (2)
Merge branch 'master' of https://github.com/AndersenLab/Variant-Caller-Pipeline

Conflicts:
	.gitignore
adding cluster scripts
ignore sam files
Ignore fq.gz
ignore .bam.zip
git ignore messed up
fix
Add manifest and strain accounting
Delete select files from manifest
filenames added