Schumer lab: Processed files available on Oak

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Previously generated tsv files

Previously generated ancestry tsv files can be found here:

/oak/stanford/groups/schumer/data/Ancestry_tsv_results_files

Remember to put your cfg files in as well with matched names so future lab members can know what parameters were used


Currently available ancestry tsv files in this directory:

ancestry-probs-par1_allchrs_allF2_orlater_stocktanks_March2019.tsv ancestry-probs-par2_allchrs_allF2_orlater_stocktanks_March2019.tsv

ancestry-probs-par1_serval-cat-hybrids_allchromosomes_February2019.tsv ancestry-probs-par2_serval-cat-hybrids_allchromosomes_February2019.tsv

Previously generated bam files

Mapped to the X. hellerii genome (GCA_003331165.1_Xiphophorus_hellerii-4.0_genomic.fna) with bwa mem, sorted & deduplicated with Picard tools, and indels realigned with GATK 3.4:


/oak/stanford/groups/schumer/data/Xcortezi_whole_genome_data_sc_project_HUIC_sc_and_wt/HUICXI17M01wt_read_1_allcombined.fastq.gz_xhel.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xcortezi_whole_genome_data_sc_project_HUIC_sc_and_wt/HUICXI17M03sc_read_1_allcombined.fastq.gz_xhel.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xcortezi_whole_genome_data_sc_project_HUIC_sc_and_wt/HUICXI17M05sc_read_1_allcombined.fastq.gz_xhel.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xiphophorus_species_raw_illumina_data/SRR7525605_1.fastq.gz_xhel.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xiphophorus_species_raw_illumina_data/SRR7532852_1.fastq.gz_xhel.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xiphophorus_species_raw_illumina_data/Xiphophorus-variatus-for-108-cycles-C30ULACXX_2_Read_1_passed_filter.fastq.gz_xhel.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xiphophorus_species_raw_illumina_data/X-montezumae-tamasopo-genomic-library-for-157-cycles-H5K57BCXX_2_Read_1_passed_filter.fastq.gz_xhel.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xmalinche_Quail_libraries_and_data_from_ChrisBlazier_2012-2017/Qfilter_Xm_female_merge.assembled.fastq.gz_xhel.sorted.dedup.realigned.bam


Mapped to the X. malinche 10x genome (xiphophorus_malinche_10x_14Nov2018_HyZ96.fasta) with bwa mem, sorted & deduplicated with Picard tools, and indels realigned with GATK 3.4:


/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC10F_read_1.combined.trimmed.fq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC12F_read_1.combined.trimmed.fq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC15F_read_1.combined.trimmed.fq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC17F_read_1.combined.trimmed.fq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC19F_read_1.combined.trimmed.fq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC1F_read_1.combined.trimmed.fq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC2010F06_read_1.trimmed.fq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC2010F09_read_1.trimmed.fq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC2010F18_read_1.trimmed.fq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC2010M01_read_1.combined.trimmed.fq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC2010M02_read_1.combined.trimmed.fq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC2010M03_read_1.trimmed.fq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC2F_read_1.trimmed.fq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC7F_read_1.combined.trimmed.fq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC8F_read_1.combined.trimmed.fq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/Family_father_read_1.trimmed.fq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/Family_mother_read_1.trimmed.fq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xbirchmanni_whole_genome_data_Quail_libraries_sc_and_wt_December2018/COACVI1808_FC1-6_read_1.fastq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xbirchmanni_whole_genome_data_Quail_libraries_sc_and_wt_December2018/COACVI1809_FC1-7_read_1.fastq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xbirchmanni_whole_genome_data_Quail_libraries_sc_and_wt_December2018/COACVI1810_FC1-8_read_1.fastq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xbirchmanni_whole_genome_data_Quail_libraries_sc_and_wt_December2018/COACVI1836_FC1-14_read_1.fastq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xbirchmanni_whole_genome_data_Quail_libraries_sc_and_wt_December2018/COACVI1837_FC1-15_read_1.fastq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xbirchmanni_whole_genome_data_Quail_libraries_sc_and_wt_December2018/COACVI1839_FC1-16_read_1.fastq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xcortezi_whole_genome_data_sc_project_HUIC_sc_and_wt/HUICXI17JM06wt_read_1_allcombined.fastq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xcortezi_whole_genome_data_sc_project_HUIC_sc_and_wt/HUICXI17JM07sc_read_1_allcombined.fastq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xcortezi_whole_genome_data_sc_project_HUIC_sc_and_wt/HUICXI17M01wt_read_1_allcombined.fastq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xcortezi_whole_genome_data_sc_project_HUIC_sc_and_wt/HUICXI17M03sc_read_1_allcombined.fastq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xcortezi_whole_genome_data_sc_project_HUIC_sc_and_wt/HUICXI17M04wt_read_1_allcombined.fastq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xcortezi_whole_genome_data_sc_project_HUIC_sc_and_wt/HUICXI17M05sc_read_1_allcombined.fastq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xiphophorus_species_raw_illumina_data/Xiphophorus-variatus-for-108-cycles-C30ULACXX_2_Read_1_passed_filter.fastq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xiphophorus_species_raw_illumina_data/X-montezumae-tamasopo-genomic-library-for-108-cycles-C7M4MACXX_2_Read_1_passed_filter.fastq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xiphophorus_species_raw_illumina_data/X-montezumae-tamasopo-genomic-library-for-157-cycles-H5K57BCXX_2_Read_1_passed_filter.fastq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xmalinche_Quail_libraries_and_data_from_ChrisBlazier_2012-2017/Qfilter_Xmal_male_merge_78mil.fastq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xmalinche_Quail_libraries_and_data_from_ChrisBlazier_2012-2017/Qfilter_Xm_female_merge.assembled.fastq.gz_xmal-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xmalinche_Quail_libraries_and_data_from_ChrisBlazier_2012-2017/TETI_read_1.fq.gz_xmal-10x.sorted.dedup.realigned.bam


Mapped to the X. birchmanni 10x genome (xiphophorus_birchmanni_10x_12Sep2018_yDAA6.fasta) with bwa mem, sorted & deduplicated with Picard tools, and indels realigned with GATK 3.4:


/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC10F_read_1.combined.trimmed.fq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC11F_read_1.combined.trimmed.fq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC12F_read_1.combined.trimmed.fq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC14F_read_1.trimmed.fq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC15F_read_1.combined.trimmed.fq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC16F_read_1.combined.trimmed.fq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC17F_read_1.combined.trimmed.fq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC19F_read_1.combined.trimmed.fq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC1F_read_1.combined.trimmed.fq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC2010F06_read_1.trimmed.fq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC2010F09_read_1.trimmed.fq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC2010F18_read_1.trimmed.fq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC2010M01_read_1.combined.trimmed.fq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC2010M02_read_1.combined.trimmed.fq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC2010M03_read_1.trimmed.fq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC2F_read_1.trimmed.fq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC7F_read_1.combined.trimmed.fq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/COAC8F_read_1.combined.trimmed.fq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/Family_father_read_1.trimmed.fq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/Family_mother_read_1.trimmed.fq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/Family_offspring11_read_1.trimmed.fq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/Family_offspring12_read_1.trimmed.fq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/Family_offspring13_read_1.trimmed.fq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/LD_map_Xbirchmanni_Recombination_paper_Princeton_2016/Family_offspring14_read_1.trimmed.fq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xbirchmanni_whole_genome_data_Quail_libraries_sc_and_wt_December2018/COACVI1808_FC1-6_read_1.fastq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xbirchmanni_whole_genome_data_Quail_libraries_sc_and_wt_December2018/COACVI1809_FC1-7_read_1.fastq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xbirchmanni_whole_genome_data_Quail_libraries_sc_and_wt_December2018/COACVI1810_FC1-8_read_1.fastq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xbirchmanni_whole_genome_data_Quail_libraries_sc_and_wt_December2018/COACVI1836_FC1-14_read_1.fastq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xbirchmanni_whole_genome_data_Quail_libraries_sc_and_wt_December2018/COACVI1837_FC1-15_read_1.fastq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xbirchmanni_whole_genome_data_Quail_libraries_sc_and_wt_December2018/COACVI1839_FC1-16_read_1.fastq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xcortezi_whole_genome_data_sc_project_HUIC_sc_and_wt/HUICXI17JM06wt_read_1_allcombined.fastq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xcortezi_whole_genome_data_sc_project_HUIC_sc_and_wt/HUICXI17JM07sc_read_1_allcombined.fastq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xcortezi_whole_genome_data_sc_project_HUIC_sc_and_wt/HUICXI17M01wt_read_1_allcombined.fastq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xcortezi_whole_genome_data_sc_project_HUIC_sc_and_wt/HUICXI17M03sc_read_1_allcombined.fastq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xcortezi_whole_genome_data_sc_project_HUIC_sc_and_wt/HUICXI17M04wt_read_1_allcombined.fastq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xcortezi_whole_genome_data_sc_project_HUIC_sc_and_wt/HUICXI17M05sc_read_1_allcombined.fastq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xiphophorus_species_raw_illumina_data/SRR7525605_1.fastq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xiphophorus_species_raw_illumina_data/SRR7532852_1.fastq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xiphophorus_species_raw_illumina_data/Xiphophorus-variatus-for-108-cycles-C30ULACXX_2_Read_1_passed_filter.fastq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xiphophorus_species_raw_illumina_data/X-montezumae-tamasopo-genomic-library-for-108-cycles-C7M4MACXX_2_Read_1_passed_filter.fastq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xiphophorus_species_raw_illumina_data/X-montezumae-tamasopo-genomic-library-for-157-cycles-H5K57BCXX_2_Read_1_passed_filter.fastq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xiphophorus_species_raw_illumina_data/X-nezzy-galliots-3-genomic-library-for-108-cycles-C7M4MACXX_1_Read_1_passed_filter.fastq.gz_xbir-10x.sorted.dedup.realigned.bam

/oak/stanford/groups/schumer/data/Xmalinche_Quail_libraries_and_data_from_ChrisBlazier_2012-2017/Qfilter_Xm_female_merge.assembled.fastq.gz_xbir-10x.sorted.dedup.realigned.bam