lananhle / ppipilot Public

forked from adamallo/ppipilot

Scripts used for a specific pilot project (intended for personal use only)

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Name		Name	Last commit message	Last commit date
Latest commit History 16 Commits
LICENSE.md		LICENSE.md
README.md		README.md
bamqc.sh		bamqc.sh
combdepth.pl		combdepth.pl
combineBamPerSample.sh		combineBamPerSample.sh
depth.sh		depth.sh
depth_hist.sh		depth_hist.sh
duplexmetrics.sh		duplexmetrics.sh
fastqc.sh		fastqc.sh
filtercalls.sh		filtercalls.sh
flagstat.sh		flagstat.sh
gatk_coverage.sbatch		gatk_coverage.sbatch
gatk_coverage_exome.sbatch		gatk_coverage_exome.sbatch
gatk_coverage_exome_brc83.sbatch		gatk_coverage_exome_brc83.sbatch
indelrealigner.sh		indelrealigner.sh
index.sh		index.sh
launch_contamination.sh		launch_contamination.sh
launch_coverage.sh		launch_coverage.sh
launch_filtercalls.sh		launch_filtercalls.sh
launch_lofreq.sh		launch_lofreq.sh
launch_mutect1.sh		launch_mutect1.sh
launch_mutect2.sh		launch_mutect2.sh
launch_pileupsummaries.sh		launch_pileupsummaries.sh
launch_pon.sh		launch_pon.sh
launch_strelka2.sh		launch_strelka2.sh
lofreq.sh		lofreq.sh
makeBamPerRun.sh		makeBamPerRun.sh
make_contamination.sh		make_contamination.sh
make_gpop_freqs.sh		make_gpop_freqs.sh
make_pileups_sq.sh		make_pileups_sq.sh
make_pileupsummaries.sh		make_pileupsummaries.sh
mutect1.sh		mutect1.sh
mutect2.sh		mutect2.sh
mutect2_tonly.sh		mutect2_tonly.sh
oneliners.sh		oneliners.sh
pipeline.sh		pipeline.sh
pon.sh		pon.sh
preprocess_sq.sh		preprocess_sq.sh
qc.sh		qc.sh
realign.sh		realign.sh
sequenza-utils.py		sequenza-utils.py
sequenza.R		sequenza.R
sequenza.sh		sequenza.sh
strelka2.sh		strelka2.sh
sumcov.sh		sumcov.sh