Name	Name	Last commit message	Last commit date
Latest commit ekg fixed interval specification Oct 11, 2014 01c3012 · Oct 11, 2014 History 31 Commits
align	align	updated swe, fixed more functions	Oct 10, 2014
apply_bed_filter	apply_bed_filter	fully working exome pipeline	Sep 16, 2014
bin	bin	updated swe, fixed more functions	Oct 10, 2014
bqsr	bqsr	hacking around, adding streaming duplicate marking, freebayes only	Oct 7, 2014
combine	combine	checkpoint, testing now	Oct 10, 2014
combine_vcf	combine_vcf	checkpoint, testing now	Oct 10, 2014
freebayes	freebayes	fixed interval specification	Oct 11, 2014
gatk-hc	gatk-hc	fixed interval specification	Oct 11, 2014
gatk-ug	gatk-ug	fixed interval specification	Oct 11, 2014
glia	glia	fixed interval specification	Oct 11, 2014
platypus	platypus	fixed interval specification	Oct 11, 2014
split_chr	split_chr	missed some files...	Oct 10, 2014
split_fastq	split_fastq	missed some files...	Oct 10, 2014
vqsr	vqsr	swe fix to avoid EC problems	Sep 21, 2014
.gitignore	.gitignore	added .gitignore	Sep 23, 2014
GATK-pdf.pdf	GATK-pdf.pdf	added pipeline pdf	Sep 15, 2014
GenomeAnalysisTKLite.jar	GenomeAnalysisTKLite.jar	swe fix to avoid EC problems	Sep 21, 2014
HG00096.lowcov.settings	HG00096.lowcov.settings	checkpoint, testing now	Oct 10, 2014
LICENSE	LICENSE	swe fix to avoid EC problems	Sep 21, 2014
MarkDuplicates.jar	MarkDuplicates.jar	updated to also use GATK HaplotypeCaller	Oct 9, 2014
README.md	README.md	Initial commit	Sep 15, 2014
bin.tar.gz	bin.tar.gz	added compatibility with GATK 3.0	Sep 19, 2014
download_reference.sh	download_reference.sh	fully working exome pipeline	Sep 16, 2014
exome.settings	exome.settings	updated to also use GATK HaplotypeCaller	Oct 9, 2014
general_settings.sh	general_settings.sh	fixed align memory problem	Sep 18, 2014
install_dependencies.sh	install_dependencies.sh	fixed install_dependencies.sh	Sep 17, 2014
pipeline.sh	pipeline.sh	updated swe, fixed more functions	Oct 10, 2014
pre_script.sh	pre_script.sh	checkpoint, testing now	Oct 10, 2014
snyderome.settings	snyderome.settings	switch to GATK light	Sep 24, 2014
swe	swe	fully working exome pipeline	Sep 16, 2014

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