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data_summary_for_figures
test_fixtures
% ClinVar Miscalled Cs.png
% Miscalled Cs GRCh38 vs. T2T.png
%Miscalled Cs.png
.gitignore
.gitignore~
4641904citation.bib
Chrom_fig.png
Chrom_fig.svg
Figure 1-4.svg
GRCh38 vs T2T Total Calls.png
GRCh38 vs T2T.png
LICENSE
Methyl Miscalls.png
Methylation Data.twb
Miscalled Clinvar Genes.png
Miscalled Genes.png
Miscalls ClinVar.png
Miscalls Fig.png
Miscalls Overview.png
Miscalls in ClinVar.png
Over-Underfiltered Cs.png
Overall Called Cs.png
Overfiltered-Underfiltered Calls Linear.png
Overfiltered-Underfiltered Calls Logarithmic.png
README.md
Resolved Calls.pdf
Resolved Calls.png
T2T Overview.png
Untitled drawing-2 copy.svg
Untitled drawing-2.svg
Untitled drawing-2.svg.2021_08_10_12_05_25.0.svg
add_params.py
analysis_bam.png
analysis_bam.svg
analysis_clinvar.svg
analysis_postproc.svg
analysis_preproc.svg
chr1_148819799-148820800.svg
chr1_148819799-148820800_a.svg
chr1_148823039-148824040.svg
chr2_110091420-110092421.svg
chr2_110091420-110092421_a.svg
chromosomePlot.R
chroms_ideogram.png
chroms_parts_combined copy.png
chroms_parts_combined.png
chroms_parts_combined_blue.png
clinvar.nf
count_calls.py
drawing.svg
fig copy 2.png
fig copy.png
fig.png
fig.svg
fig1_svg.svg
fig2_svg.svg
fig3_svg.svg
fig4_svg copy.svg
fig4_svg.svg
fig4_svg.svg.2021_10_04_15_02_57.0.svg
igv_snapshot.svg
kumar_correcting_methylation_calling.pdf
mbias_fig.svg
methylation workflow bams.dot
methylation workflow clinvar.dot
methylation workflow postproc.dot
methylation workflow preproc.dot
miscalls_full.nf
miscalls_one.nf
miscalls_pair.nf
over_underfilt.png
paper.lyx
procfig_1.dot
procfig_1.svg
procfig_2.dot
procfig_2.svg
realign workflow.dot
realign.nf
realign.svg
summarize_line_counts.sh
to_do_list.txt

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