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exome_workflow_v02
exome_workflow_v02
 
 
.gitignore
.gitignore
 
 
ACMG_56_2016_07_11.txt
ACMG_56_2016_07_11.txt
 
 
HGVS_GeneName_to_NM.py
HGVS_GeneName_to_NM.py
 
 
README.md
README.md
 
 
bamToBigWig.sh
bamToBigWig.sh
 
 
bedGraphToBigWig
bedGraphToBigWig
 
 
bedtools_bamtofastq.sh
bedtools_bamtofastq.sh
 
 
cat_NISC_vcf.sh
cat_NISC_vcf.sh
 
 
clinvar_vcf_to_gene_disease_table.py
clinvar_vcf_to_gene_disease_table.py
 
 
convert_chrNames.sh
convert_chrNames.sh
 
 
convert_hg19_bed_to_b37.py
convert_hg19_bed_to_b37.py
 
 
create_gemini_db.sh
create_gemini_db.sh
 
 
exac.scores.bed.gz
exac.scores.bed.gz
 
 
exac.scores.bed.gz.tbi
exac.scores.bed.gz.tbi
 
 
eye_genes_disease.bed.gz
eye_genes_disease.bed.gz
 
 
eye_genes_disease.bed.gz.tbi
eye_genes_disease.bed.gz.tbi
 
 
family_based_vcf.sh
family_based_vcf.sh
 
 
fetchChromSizes.sh
fetchChromSizes.sh
 
 
gemini_exomes.toml
gemini_exomes.toml
 
 
gemini_exomes_full_anno.toml
gemini_exomes_full_anno.toml
 
 
gene_gtf_to_bed.sh
gene_gtf_to_bed.sh
 
 
gnomad_csv_to_vcf.py
gnomad_csv_to_vcf.py
 
 
gsort_linux_amd64
gsort_linux_amd64
 
 
gtf_to_bed.sh
gtf_to_bed.sh
 
 
hg19_bwa_gatk_gemini_files_to_keep.sh
hg19_bwa_gatk_gemini_files_to_keep.sh
 
 
join_on_multiple_fields.py
join_on_multiple_fields.py
 
 
kallisto_quant.sh
kallisto_quant.sh
 
 
kallisto_quant_single_stream.sh
kallisto_quant_single_stream.sh
 
 
kallisto_quant_stream.sh
kallisto_quant_stream.sh
 
 
prep_VCF_for_gemini.sh
prep_VCF_for_gemini.sh
 
 
prepend.sh
prepend.sh
 
 
query_gemini.py
query_gemini.py
 
 
query_gemini_caseyFreebayes.py
query_gemini_caseyFreebayes.py
 
 
readme.md
readme.md
 
 
runR.sh
runR.sh
 
 
run_GATK_PhaseByTransmission.sh
run_GATK_PhaseByTransmission.sh
 
 
run_LUMPY.sh
run_LUMPY.sh
 
 
run_Picard_LiftoverVcf.sh
run_Picard_LiftoverVcf.sh
 
 
run_Picard_MarkDuplicates.sh
run_Picard_MarkDuplicates.sh
 
 
run_Picard_SamToFASTQ.sh
run_Picard_SamToFASTQ.sh
 
 
run_RTG_vcfeval.sh
run_RTG_vcfeval.sh
 
 
run_STAR_mapping.sh
run_STAR_mapping.sh
 
 
run_bam2fastq.sh
run_bam2fastq.sh
 
 
run_fastqc.sh
run_fastqc.sh
 
 
run_freebayes.sh
run_freebayes.sh
 
 
run_kallisto_quant.sh
run_kallisto_quant.sh
 
 
run_picard_AddOrReplaceReadGroups.sh
run_picard_AddOrReplaceReadGroups.sh
 
 
run_qorts.sh
run_qorts.sh
 
 
run_vcf-merge.sh
run_vcf-merge.sh
 
 
sampler.py
sampler.py
 
 
sbatch_command_withRG_align_fastq.py
sbatch_command_withRG_align_fastq.py
 
 
split_matrix_by_col.py
split_matrix_by_col.py
 
 
stream_fastq_ftp.sh
stream_fastq_ftp.sh
 
 
trim_NISC_vcf.sh
trim_NISC_vcf.sh
 
 
vcf_qual_depth_filter.py
vcf_qual_depth_filter.py
 
 
vcf_sample_stripper.sh
vcf_sample_stripper.sh
 
 
vcf_split_n.sh
vcf_split_n.sh
 
 
vcf_to_geminiDB.sh
vcf_to_geminiDB.sh
 
 
vt_normalize.sh
vt_normalize.sh
 
 

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biowulf2-bin

~/bin on biowulf2.nih.gov Scripts and pipelines largely specific to biowulf2.nih.gov

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