short_read_analysis

general tools for handling short read data; mostly quite specific to odyssey cluster

Name		Name	Last commit message	Last commit date
Latest commit History 55 Commits
#get_gdoc_as_dict_stream.py#		#get_gdoc_as_dict_stream.py#
#merge_bams_with_headers_samtools.py#		#merge_bams_with_headers_samtools.py#
MLaf.py		MLaf.py
README.md		README.md
__init__.py		__init__.py
__init__.pyc		__init__.pyc
add_phenotypes_to_map.py		add_phenotypes_to_map.py
add_rg_and_sort_bam_by_ref.py		add_rg_and_sort_bam_by_ref.py
add_rg_to_sam.py		add_rg_to_sam.py
bam_RG_from_index.py		bam_RG_from_index.py
bcl_to_fastq.py		bcl_to_fastq.py
blast_from_rad_clusters.py		blast_from_rad_clusters.py
enclosure_helpers.py		enclosure_helpers.py
enclosure_helpers.pyc		enclosure_helpers.pyc
estimate_synteny_from_map.py		estimate_synteny_from_map.py
extract_genotypes_from_mclgr.py		extract_genotypes_from_mclgr.py
extract_genotypes_from_mclgr.pyc		extract_genotypes_from_mclgr.pyc
fastPHASE_to_ms.py		fastPHASE_to_ms.py
fasta_to_fastphase.py		fasta_to_fastphase.py
fastq_to_vcf.py		fastq_to_vcf.py
fastq_to_vcf.pyc		fastq_to_vcf.pyc
fastq_to_vcf.py~		fastq_to_vcf.py~
fastq_to_vcf_bwa.py		fastq_to_vcf_bwa.py
fastq_to_vcf_bwa.py~		fastq_to_vcf_bwa.py~
filter_reads_by_mean_qual.py		filter_reads_by_mean_qual.py
fit_gaussian_to_cluster_rep.py		fit_gaussian_to_cluster_rep.py
fix_fastq_headers_for_stampy.py		fix_fastq_headers_for_stampy.py
fq1_to_fq4.py		fq1_to_fq4.py
fq4_to_fq1.py		fq4_to_fq1.py
get_bam_rg_by_sample.py		get_bam_rg_by_sample.py
get_bam_rg_by_sample.py~		get_bam_rg_by_sample.py~
join_reads.py		join_reads.py
make_indexes.py		make_indexes.py
map_reads_by_indiv-bwastampy.py		map_reads_by_indiv-bwastampy.py
map_reads_by_indiv-bwastampy.py~		map_reads_by_indiv-bwastampy.py~
map_reads_by_indiv-stampy.py		map_reads_by_indiv-stampy.py
map_reads_by_indiv-stampy.py~		map_reads_by_indiv-stampy.py~
map_reads_by_indiv_stampy.py		map_reads_by_indiv_stampy.py
map_reads_by_indiv_stampy.pyc		map_reads_by_indiv_stampy.pyc
merge_bams_with_headers_samtools.py		merge_bams_with_headers_samtools.py
merge_identical_seqs.py		merge_identical_seqs.py
merge_map_csv.py		merge_map_csv.py
merge_read_Sample_by_index.py		merge_read_Sample_by_index.py
merge_sams_no_validation.py		merge_sams_no_validation.py
merge_sams_with_validation.py		merge_sams_with_validation.py
merge_vcf_parts.py		merge_vcf_parts.py
pct_barcoded.py		pct_barcoded.py
random_wigs.py		random_wigs.py
random_wigs_controller.py		random_wigs_controller.py
read_quality_statistics.py		read_quality_statistics.py
realign_reduce_bam.py		realign_reduce_bam.py
resolve_multiallelic_vcf.py		resolve_multiallelic_vcf.py
retired.tar		retired.tar
samtools_cmd_by_sample.py		samtools_cmd_by_sample.py
samtools_cmd_by_sample.py~		samtools_cmd_by_sample.py~
simulate_rad_recovery.py		simulate_rad_recovery.py
split_tags.py		split_tags.py
summarize_bam.py		summarize_bam.py
summarize_hybsel_bam.py		summarize_hybsel_bam.py
variant_detection.py		variant_detection.py
variant_detection.pyc		variant_detection.pyc
variant_detection.py~		variant_detection.py~
wigs_by_locus_controller.py		wigs_by_locus_controller.py

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