Name		Name	Last commit message	Last commit date
Latest commit History 3 Commits
R		R
gender_inference		gender_inference
292individuals.py		292individuals.py
3dplot.py		3dplot.py
LICENSE		LICENSE
README.md		README.md
addPASS.py		addPASS.py
add_chr_to_fasta.py		add_chr_to_fasta.py
addreplacereadgroup.py		addreplacereadgroup.py
addrsid.py		addrsid.py
annotate_vcf_with_all.py		annotate_vcf_with_all.py
annotate_vcf_with_dbsnp135.py		annotate_vcf_with_dbsnp135.py
annovar.py		annovar.py
annovar2vcf.py		annovar2vcf.py
bam_metrics.py		bam_metrics.py
beagle.py		beagle.py
bioinfo_github.txt		bioinfo_github.txt
bwa-mem.py		bwa-mem.py
bwa.py		bwa.py
bwa_0.6.1.py		bwa_0.6.1.py
cancer_pipeline.py		cancer_pipeline.py
conifer.py		conifer.py
dbsnp_bitfield.py		dbsnp_bitfield.py
define_values.sh		define_values.sh
detect_target.py		detect_target.py
diseasegene.sh		diseasegene.sh
edit_1092exomes.py		edit_1092exomes.py
exome_pipeline.py		exome_pipeline.py
extrac_individuals_from_EUR_AFR_AMR.py		extrac_individuals_from_EUR_AFR_AMR.py
extract_exomes.py		extract_exomes.py
extract_vcfs.py		extract_vcfs.py
fastq_ill_2_fastq_std.py		fastq_ill_2_fastq_std.py
filter_analysis.py		filter_analysis.py
filter_atcg_ped.py		filter_atcg_ped.py
find_pathogenic_clinvar.py		find_pathogenic_clinvar.py
finddenovo.py		finddenovo.py
fq_all2std.pl		fq_all2std.pl
frappe.py		frappe.py
gatk.1.1.py		gatk.1.1.py
gatk.py		gatk.py
gatk2.3.4.py		gatk2.3.4.py
gatk2.3.py		gatk2.3.py
gatk_latest.py		gatk_latest.py
getfreq.py		getfreq.py
group_by_extensions.py		group_by_extensions.py
haplotypecaller.py		haplotypecaller.py
helper.py		helper.py
identify_individuals.py		identify_individuals.py
join_annovar_vcf.py		join_annovar_vcf.py
kegg_pathway.py		kegg_pathway.py
king_pedmap.py		king_pedmap.py
kinship.py		kinship.py
liftdbsnp138.py		liftdbsnp138.py
lobSTR.py		lobSTR.py
lobSTR_annotation.py		lobSTR_annotation.py
lobSTR_to_vcf.py		lobSTR_to_vcf.py
local2ref.py		local2ref.py
merge_pedmap.py		merge_pedmap.py
merge_vcfs.py		merge_vcfs.py
merge_vcfs_gatk.py		merge_vcfs_gatk.py
niceplot.R		niceplot.R
parse_bams.py		parse_bams.py
parse_gencode.py		parse_gencode.py
parse_morbidmap.py		parse_morbidmap.py
phasing.py		phasing.py
polyphen2.py		polyphen2.py
process_bam.py		process_bam.py
provean.py		provean.py
readbackphashing.py		readbackphashing.py
reap.py		reap.py
reap_admixture.py		reap_admixture.py
reap_admixture_1092exomes.py		reap_admixture_1092exomes.py
reap_admixture_pedmap.py		reap_admixture_pedmap.py
recodemap.py		recodemap.py
recodeped.py		recodeped.py
relatedness.py		relatedness.py
remove_missing_markers.py		remove_missing_markers.py
remove_rs.py		remove_rs.py
remove_xy.py		remove_xy.py
remove_y.py		remove_y.py
reorderbam.py		reorderbam.py
reordersam.py		reordersam.py
samtools_parallel.sh		samtools_parallel.sh
select_random_snps.py		select_random_snps.py
settings.py		settings.py
sift.py		sift.py
snps_omim.py		snps_omim.py
solid_exome_pipeline.py		solid_exome_pipeline.py
sort_vcf.py		sort_vcf.py
tcga_to_dnanexus.py		tcga_to_dnanexus.py
test.py		test.py
test_r.py		test_r.py
trio_unifiergenotyper.py		trio_unifiergenotyper.py
unifiergenotyper.py		unifiergenotyper.py
unifiergenotyper_cancer.py		unifiergenotyper_cancer.py
unifiergenotyper_gvcf.py		unifiergenotyper_gvcf.py
unifiergenotyper_hg18.py		unifiergenotyper_hg18.py
unifiergenotyper_hg18_notarget.py		unifiergenotyper_hg18_notarget.py
unifiergenotyper_indel.py		unifiergenotyper_indel.py
unifiergenotyper_notarget.py		unifiergenotyper_notarget.py

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bioinformatics_scripts

Some Python/R/* scripts for bioinformatics I developed

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raonyguimaraes/bioinformatics_scripts

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