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#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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short_read_analysis

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

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

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