Name		Name	Last commit message	Last commit date
Latest commit History 252 Commits
Data Exploration		Data Exploration
11_DUPs_yesmaybeallcurators_anyoverlap.csv		11_DUPs_yesmaybeallcurators_anyoverlap.csv
200ksnparray.eigenvec		200ksnparray.eigenvec
200ksnparrayplink2.eigenvec		200ksnparrayplink2.eigenvec
200ksnparrayplink2_b.eigenvec		200ksnparrayplink2_b.eigenvec
45_DUPs_yesmaybecurator1_100percentoverlap.csv		45_DUPs_yesmaybecurator1_100percentoverlap.csv
45_DUPs_yesmaybecurator1_anyoverlap.csv		45_DUPs_yesmaybecurator1_anyoverlap.csv
DUPs_3842.csv		DUPs_3842.csv
DUPs_3842_Jay.bed		DUPs_3842_Jay.bed
DUPs_3842_Jay.cov.pca		DUPs_3842_Jay.cov.pca
DUPs_3842_plusone.csv		DUPs_3842_plusone.csv
Extract_SV_regions_PCA_Part1to4.ipynb		Extract_SV_regions_PCA_Part1to4.ipynb
GATK_SelectVariants_INDEL_VariantFiltration_FS200_onlychrm_nolargeSVs.ann.genes.txt		GATK_SelectVariants_INDEL_VariantFiltration_FS200_onlychrm_nolargeSVs.ann.genes.txt
GATK_SelectVariants_INDEL_VariantFiltration_FS200_onlychrm_nolargeSVs.ann.html		GATK_SelectVariants_INDEL_VariantFiltration_FS200_onlychrm_nolargeSVs.ann.html
GATK_SelectVariants_INDEL_VariantFiltration_FS200_onlychrm_nolargeSVs.eigenvec		GATK_SelectVariants_INDEL_VariantFiltration_FS200_onlychrm_nolargeSVs.eigenvec
GCA_001700915.1_Passer_domesticus-1.0_genomic.fasta.fai		GCA_001700915.1_Passer_domesticus-1.0_genomic.fasta.fai
HS.sample.csv		HS.sample.csv
HS.sample_allsparrows.csv		HS.sample_allsparrows.csv
HS.sample_onlyPdomesticus.csv		HS.sample_onlyPdomesticus.csv
INVS_allsparrows_yes.csv		INVS_allsparrows_yes.csv
INVs_goodgenos_allsparrowsJay.bed		INVs_goodgenos_allsparrowsJay.bed
Plotting_PCA_for_Downsampled_SNPs.ipynb		Plotting_PCA_for_Downsampled_SNPs.ipynb
Plotting_Size_Histograms_for_SVs.ipynb		Plotting_Size_Histograms_for_SVs.ipynb
README.md		README.md
SNParraypops.csv		SNParraypops.csv
SV_altgenos.bed		SV_altgenos.bed
Snakefile_1		Snakefile_1
all_rejected.txt		all_rejected.txt
allgenos_48Pdom_DEL_samplotML.csv		allgenos_48Pdom_DEL_samplotML.csv
alluncurated.txt		alluncurated.txt
annodel_100percentoverlap.csv		annodel_100percentoverlap.csv
annodel_anyoverlap.txt		annodel_anyoverlap.txt
annodup_100percentoverlap.csv		annodup_100percentoverlap.csv
annodup_anyoverlap.txt		annodup_anyoverlap.txt
annofix.ipynb		annofix.ipynb
annoinv_anyoverlap.txt		annoinv_anyoverlap.txt
annotation.gff		annotation.gff
annotations_namesfixed.gff		annotations_namesfixed.gff
chromosome_numbers.csv		chromosome_numbers.csv
circos_R.ipynb		circos_R.ipynb
dels_genesonly_anyoverlaptab.bed		dels_genesonly_anyoverlaptab.bed
dups_genesonly_anyoverlaptab.bed		dups_genesonly_anyoverlaptab.bed
dups_genesonly_anyoverlaptab.csv		dups_genesonly_anyoverlaptab.csv
dups_genesonly_anyoverlaptab_chr20only.csv		dups_genesonly_anyoverlaptab_chr20only.csv
environment.yml		environment.yml
geno_plink_filter1400.eigenvec		geno_plink_filter1400.eigenvec
geno_plink_filter15000.eigenvec		geno_plink_filter15000.eigenvec
geno_plink_filter20.eigenvec		geno_plink_filter20.eigenvec
geno_plink_filter2000.eigenvec		geno_plink_filter2000.eigenvec
geno_plink_filter300.eigenvec		geno_plink_filter300.eigenvec
geno_plink_filter6700.eigenvec		geno_plink_filter6700.eigenvec
good_INVs_Jay.cov.pca		good_INVs_Jay.cov.pca
house_sparrow_genome_assembly-18-11-14_masked.fa.fai		house_sparrow_genome_assembly-18-11-14_masked.fa.fai
indels.filtered.gatk.eigenvec		indels.filtered.gatk.eigenvec
indels.filtered_onlychrm_nolargeSVsGATK.eigenvec		indels.filtered_onlychrm_nolargeSVsGATK.eigenvec
indels_anyoverlap_genesonlytab.csv		indels_anyoverlap_genesonlytab.csv
indelsfilteredchrm_nolargeSVs.eigenvec		indelsfilteredchrm_nolargeSVs.eigenvec
invs_genesonly_anyoverlaptab.bed		invs_genesonly_anyoverlaptab.bed
jay_yesmaybe_INVs_tabs_plusone_POS_tab.csv		jay_yesmaybe_INVs_tabs_plusone_POS_tab.csv
jay_yesmaybe_genos_INVs.bed		jay_yesmaybe_genos_INVs.bed
large_curated_DUPs_DELs.csv		large_curated_DUPs_DELs.csv
namefix_SVsingenes.ipynb		namefix_SVsingenes.ipynb
pop.info		pop.info
raw_report_del_dec26_2020.tsv		raw_report_del_dec26_2020.tsv
raw_report_dup_dec26_2020.tsv		raw_report_dup_dec26_2020.tsv
raw_report_inv_dec26_2020.tsv		raw_report_inv_dec26_2020.tsv
shortindels_anyoverlapwithgenes.csv		shortindels_anyoverlapwithgenes.csv
shortindels_anyoverlapwithgenes.txt		shortindels_anyoverlapwithgenes.txt
snprelatesamples_pcandgsd.cov		snprelatesamples_pcandgsd.cov
snprelatesamples_simplepca.cov		snprelatesamples_simplepca.cov
yesallintersect.txt		yesallintersect.txt
yesmaybeDUP_curator1_dec292020.csv		yesmaybeDUP_curator1_dec292020.csv
yesmaybe_DEL_curator1.tsv		yesmaybe_DEL_curator1.tsv
yesmaybe_DEL_curator1_processed.csv		yesmaybe_DEL_curator1_processed.csv
yesmaybe_DUP_curator1.tsv		yesmaybe_DUP_curator1.tsv
yesmaybe_DUP_curator1_processed.csv		yesmaybe_DUP_curator1_processed.csv
yesmaybe_INV_curator1.tsv		yesmaybe_INV_curator1.tsv
yesmaybe_INV_curator1_processed.csv		yesmaybe_INV_curator1_processed.csv
yesmaybeall_DUP_anyoverlap_genesonly.csv		yesmaybeall_DUP_anyoverlap_genesonly.csv
yesmaybeallintersect.txt		yesmaybeallintersect.txt

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Genomic Landscape of Structural Variation in Passer domesticus

Structural Variant Calling and Visual Curation

Snakefile: BWA alignment and GATK pipeline

Followed by: Structural variant calling and genotyping with smoove(more here)

Data Exploration

JupyterNotebooks for executing all steps, from extracting curated variants from raw PlotCritic reports to final plotting in Python3. These need to be run in the order presented below.

Notebook #1, Part 1: Intersecting and plotting a PCA for all Deletions that were given "Yes" by all four curators.

Click to open

Notebook #1, Parts 2 to 4: Intersecting and plotting a PCA for all Deletions that were given either "Yes" or "Maybe" by all four curators; plotting all of the remaining SVs that were rejected by all four curators; and plotting all raw Uncurated Deletions.

Click to open

Notebook #2: Plotting Size Histograms for SVs

Click to open

Notebook #3: Downsampling SNPs in PLINK and plotting PCAs to compare to similarly-sized SV-callsets

Click to open

Notebook #4: Circos Plot in R Click to open

gdaviduu/House-Sparrow-Genome-Analysis

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