GitHub - pengweixing/ecDNA-on-GCA: scripts involved in GCA paper

Branches Tags

Name		Name	Last commit message	Last commit date
Latest commit History 2 Commits
hg19_10kb_chr		hg19_10kb_chr
GII_calculating.sh		GII_calculating.sh
bamtowindow.sh		bamtowindow.sh
delly.sh		delly.sh
delly.vcf2ShatterSeek.py		delly.vcf2ShatterSeek.py
ecDNA_distribution_heamap_plot.r		ecDNA_distribution_heamap_plot.r
ecDNA_distribution_over_whole_genome.py		ecDNA_distribution_over_whole_genome.py
ecDNA_distribution_plot.r		ecDNA_distribution_plot.r
filter_CNV_for_ecDNAcalling.sh		filter_CNV_for_ecDNAcalling.sh
maftool.r		maftool.r
mapping.sh		mapping.sh
merge.novobreak.delly.py		merge.novobreak.delly.py
novobreak.sh		novobreak.sh
plot.alcohol.r		plot.alcohol.r
plot.family.r		plot.family.r
plot_EGFR.r		plot_EGFR.r
plot_ERBB2_protein_survival.r		plot_ERBB2_protein_survival.r
plot_FGFR2.sh		plot_FGFR2.sh
plot_survival.r		plot_survival.r
readme.txt		readme.txt
run_circle_seq.sh		run_circle_seq.sh
run_copycat.r		run_copycat.r
run_ecDNA_call.sh		run_ecDNA_call.sh
run_shatterseek.r		run_shatterseek.r
vcf2ShatterSeek.novobreak.py		vcf2ShatterSeek.novobreak.py

Repository files navigation

bamtowindow.sh  prepare for cnv calling
delly.sh    for SV calling
ecDNA_distribution_heamap_plot.r  plot ecDNA distribution with heatmap across whole genome on 36 samples
ecDNA_distribution_over_whole_genome.py   prepare files for the ecDNA_distribution_heamap_plot.r
ecDNA_distribution_plot.r                 plot ecDNA distribution with barplot for 36 samples
filter_CNV_for_ecDNAcalling.sh            filter CNAs generated by copycat for ecDNA calling
GII_calculating.sh			  calculating genome integrity index
maftool.r				  snp calling
merge.novobreak.delly.py		  merged the SVs of novobreak and delly
novobreak.sh				  sv calling 
plot.alcohol.r				  the relationship between alcohol consuming and ecDNA of ERBB2,EGFR,CCNE1
plot_EGFR.r				  the genome coverage information on EGFR
plot_ERBB2_protein_survival.r 		  survival time analysis for ERBB2 expression
plot.family.r				  the relationship between family history and ecDNA of ERBB2,EGFR,CCNE1
plot_FGFR2.sh				  visualization on FGFR2 region
plot_survival.r				  survival analysis for ERBB2,EGFR,CCNE1
run_circle_seq.sh			  ecDNA calling on circle_seq data
run_copycat.r				  CNV calling by copycat
run_ecDNA_call.sh			  ecDNA calling
run_shatterseek.r			  chromothripsis calling with shatterseek
vcf2ShatterSeek.novobreak.py		  change vcf file format
hg19_10kb_chr				  input for cnv calling