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CNV consensus w freec wxs #591

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merged 4 commits into from
Jul 10, 2024
Merged

CNV consensus w freec wxs #591

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322b924
revert to old bash script
jharenza Jul 6, 2024
24cf532
add freec wxs only and consensus
jharenza Jul 6, 2024
36b3679
Merge branch 'dev' into rokita/consensus-w-freec-wxs
jharenza Jul 7, 2024
34e19fe
Merge branch 'dev' into rokita/consensus-w-freec-wxs
jharenza Jul 9, 2024
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18 changes: 9 additions & 9 deletions analyses/focal-cn-file-preparation/01-add-ploidy-cnvkit.nb.html
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Original file line number Diff line number Diff line change
Expand Up @@ -1513,7 +1513,7 @@
$(this).detach().appendTo(div);

// add a show code button right above
var showCodeText = $('<span>' + (showThis ? 'Hide' : 'Code') + '</span>');
var showCodeText = $('<span>' + (showThis ? 'Hide' : 'Show') + '</span>');
var showCodeButton = $('<button type="button" class="btn btn-default btn-xs btn-secondary btn-sm code-folding-btn pull-right float-right"></button>');
showCodeButton.append(showCodeText);
showCodeButton
Expand All @@ -1539,7 +1539,7 @@
// * Change text
// * add a class for intermediate states styling
div.on('hide.bs.collapse', function () {
showCodeText.text('Code');
showCodeText.text('Show');
showCodeButton.addClass('btn-collapsing');
});
div.on('hidden.bs.collapse', function () {
Expand Down Expand Up @@ -1793,9 +1793,9 @@ <h3>Read in data</h3>
<pre class="r"><code>cnvkit_file &lt;- file.path(&quot;..&quot;, &quot;..&quot;, &quot;data&quot;, &quot;cnv-cnvkit.seg.gz&quot;)
cnvkit_df &lt;- readr::read_tsv(cnvkit_file)</code></pre>
<!-- rnb-source-end -->
<!-- rnb-message-begin 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 -->
<!-- rnb-message-begin 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 -->
<pre><code>Rows: 5106398 Columns: 7
── Column specification ─────────────────────────────────────────────────────────────────────────
── Column specification ───────────────────────────────────────────────────────────────────────────────
Delimiter: &quot;\t&quot;
chr (2): ID, chrom
dbl (5): loc.start, loc.end, num.mark, seg.mean, copy.num
Expand All @@ -1811,12 +1811,12 @@ <h3>Read in data</h3>
<pre class="r"><code>histologies_file &lt;- file.path(&quot;..&quot;, &quot;..&quot;, &quot;data&quot;, &quot;histologies-base.tsv&quot;)
histologies_df &lt;- readr::read_tsv(histologies_file, guess_max = 100000)</code></pre>
<!-- rnb-source-end -->
<!-- rnb-message-begin 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 -->
<pre><code>Rows: 47507 Columns: 56
── Column specification ─────────────────────────────────────────────────────────────────────────
<!-- rnb-message-begin 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 -->
<pre><code>Rows: 47895 Columns: 64
── Column specification ───────────────────────────────────────────────────────────────────────────────
Delimiter: &quot;\t&quot;
chr (37): Kids_First_Participant_ID, Kids_First_Biospecimen_ID, sample_id, a...
dbl (17): cell_line_passage, OS_days, EFS_days, age_at_diagnosis_days, age_a...
chr (41): Kids_First_Participant_ID, Kids_First_Biospecimen_ID, sample_id, a...
dbl (21): cell_line_passage, OS_days, EFS_days, age_at_diagnosis_days, age_a...
lgl (2): molecular_subtype, integrated_diagnosis

ℹ Use `spec()` to retrieve the full column specification for this data.
Expand Down
83 changes: 40 additions & 43 deletions analyses/focal-cn-file-preparation/02-add-ploidy-consensus.nb.html
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479 changes: 242 additions & 237 deletions analyses/focal-cn-file-preparation/03-add-cytoband-status-consensus.nb.html
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584 changes: 302 additions & 282 deletions analyses/focal-cn-file-preparation/05-define-most-focal-cn-units.nb.html
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580 changes: 304 additions & 276 deletions analyses/focal-cn-file-preparation/06-find-recurrent-calls.nb.html
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96 changes: 70 additions & 26 deletions analyses/focal-cn-file-preparation/07-consensus-annotated-merge.R
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Expand Up @@ -28,15 +28,27 @@ option_list <- list(
optparse::make_option(
c("--cnvkit_auto"),
type = "character",
default = "results/cnvkit_annotated_cn_wxs_plus_freec_tumor_autosomes.tsv.gz",
default = NULL,
help = "annotated cnvkit cnv calls on autosomes for WXS samples"
),
optparse::make_option(
c("--cnvkit_x_and_y"),
type = "character",
default = "results/cnvkit_annotated_cn_wxs_plus_freec_tumor_x_and_y.tsv.gz",
default = NULL,
help = "annotated cnvkit cnv calls on x and y for WXS samples"
),
optparse::make_option(
c("--freec_auto"),
type = "character",
default = NULL,
help = "annotated controlfreec cnv calls on autosomes for WXS samples"
),
optparse::make_option(
c("--freec_x_and_y"),
type = "character",
default = NULL,
help = "annotated controlfreec cnv calls on x and y for WXS samples"
),
optparse::make_option(
c("--consensus_auto"),
type = "character",
Expand Down Expand Up @@ -66,41 +78,73 @@ option_list <- list(
type = "character",
default = "results",
help = "path to save the final merged files"
)
),
optparse::make_option(c("--cnvkitWXS"),
type = "logical", action = "store_true", default = TRUE,
help = "flag used to indicate using cnvkit (default) or freec for WXS")
)

# Read the arguments passed
opt_parser <- optparse::OptionParser(option_list = option_list)
opt <- optparse::parse_args(opt_parser)

# Read in the files
cnvkit_auto <- data.table::fread(opt$cnvkit_auto)
cnvkit_x_and_y <- data.table::fread(opt$cnvkit_x_and_y)
consensus_auto <- data.table::fread(opt$consensus_auto)
consensus_x_and_y <- data.table::fread(opt$consensus_x_and_y)
cnv_tumor_auto <- data.table::fread(opt$cnv_tumor_auto)
cnv_tumor_x_and_y <- data.table::fread(opt$cnv_tumor_x_and_y)

# merge WGS (consensus), WXS (cnvkit), tumor only (freec) for autosomes and x_and_y respectively
merged_auto <- rbind(cnvkit_auto, consensus_auto, cnv_tumor_auto)
merged_x_and_y <- rbind(cnvkit_x_and_y, consensus_x_and_y, cnv_tumor_x_and_y)

# write out the files
readr::write_tsv(merged_auto,
file.path(opt$outdir, "consensus_wgs_plus_cnvkit_wxs_plus_freec_tumor_only_autosomes.tsv.gz"))

readr::write_tsv(merged_x_and_y,
file.path(opt$outdir, "consensus_wgs_plus_cnvkit_wxs_plus_freec_tumor_only_x_and_y.tsv.gz"))

# Merge autosomes with X and Y and output a combined file
# For the combined file, we do not need germline_sex_estimate from x_and_y
merged_x_and_y <- merged_x_and_y %>%
dplyr::select(-germline_sex_estimate)
combined <- rbind(merged_auto, merged_x_and_y)

readr::write_tsv(combined,
file.path(opt$outdir, "consensus_wgs_plus_cnvkit_wxs_plus_freec_tumor_only.tsv.gz"))

cnvkitWXS <- opt$cnvkitWXS


if (cnvkitWXS){
# read in cnvkit files
cnvkit_auto <- data.table::fread(opt$cnvkit_auto)
cnvkit_x_and_y <- data.table::fread(opt$cnvkit_x_and_y)

# merge WGS (consensus), WXS (cnvkit), tumor only (freec) for autosomes and x_and_y respectively
merged_auto <- rbind(cnvkit_auto, consensus_auto, cnv_tumor_auto)
merged_x_and_y <- rbind(cnvkit_x_and_y, consensus_x_and_y, cnv_tumor_x_and_y)
# write out the files
readr::write_tsv(merged_auto,
file.path(opt$outdir, "consensus_wgs_plus_cnvkit_wxs_plus_freec_tumor_only_autosomes.tsv.gz"))

readr::write_tsv(merged_x_and_y,
file.path(opt$outdir, "consensus_wgs_plus_cnvkit_wxs_plus_freec_tumor_only_x_and_y.tsv.gz"))

# Merge autosomes with X and Y and output a combined file
# For the combined file, we do not need germline_sex_estimate from x_and_y
merged_x_and_y <- merged_x_and_y %>%
dplyr::select(-germline_sex_estimate)
combined <- rbind(merged_auto, merged_x_and_y)

readr::write_tsv(combined,
file.path(opt$outdir, "consensus_wgs_plus_cnvkit_wxs_plus_freec_tumor_only.tsv.gz"))
} else {
freec_auto <- data.table::fread(opt$freec_auto)
freec_x_and_y <- data.table::fread(opt$freec_x_and_y)

# merge WGS (consensus), WXS (cnvkit), tumor only (freec) for autosomes and x_and_y respectively
merged_auto <- rbind(freec_auto, consensus_auto, cnv_tumor_auto)
merged_x_and_y <- rbind(freec_x_and_y, consensus_x_and_y, cnv_tumor_x_and_y)

# write out the files
readr::write_tsv(merged_auto,
file.path(opt$outdir, "consensus_wgs_plus_freec_wxs_plus_freec_tumor_only_autosomes.tsv.gz"))

readr::write_tsv(merged_x_and_y,
file.path(opt$outdir, "consensus_wgs_plus_freec_wxs_plus_freec_tumor_only_x_and_y.tsv.gz"))

# Merge autosomes with X and Y and output a combined file
# For the combined file, we do not need germline_sex_estimate from x_and_y
merged_x_and_y <- merged_x_and_y %>%
dplyr::select(-germline_sex_estimate)
combined <- rbind(merged_auto, merged_x_and_y)

readr::write_tsv(combined,
file.path(opt$outdir, "consensus_wgs_plus_freec_wxs_plus_freec_tumor_only.tsv.gz"))

}




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108 changes: 77 additions & 31 deletions analyses/focal-cn-file-preparation/run-prepare-cn.sh
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Expand Up @@ -34,51 +34,97 @@ else
histologies_file=${data_dir}/histologies.tsv
fi

echo "add ploidy to consensus"
# Prep the consensus SEG file data
Rscript --vanilla -e "rmarkdown::render('02-add-ploidy-consensus.Rmd', clean = TRUE)"

# Run annotation step for consensus file
echo "running bedtools coverage for each sample bed"
# Run snakemake script implementing `bedtools coverage` for each sample bed file in
# `scratch/cytoband_status` -- these files are generated in
# `02-add-ploidy-consensus.Rmd`
# currently runs 10 jobs in parallel, which should be fine for most implementations
snakemake -j 10 --snakefile run-bedtools.snakemake

echo "Determine the dominant status for each chromosome arm and compare with GISTIC's arm status calls"
Rscript --vanilla -e "rmarkdown::render('03-add-cytoband-status-consensus.Rmd', clean = TRUE)"

echo "Run annotation step for consensus file"
Rscript --vanilla 04-prepare-cn-file.R \
--cnv_file ${results_dir}/consensus_seg_with_status.tsv \
--gtf_file $gtf_file \
--metadata $histologies_file \
--filename_lead "consensus_seg_annotated_cn" \
--seg

echo "Define most focal units of recurrent CNVs"
Rscript --vanilla -e "rmarkdown::render('05-define-most-focal-cn-units.Rmd', clean = TRUE)"

echo "Define the recurrent calls"
Rscript --vanilla -e "rmarkdown::render('06-find-recurrent-calls.Rmd', clean = TRUE)"


# if we want to process the CNV data from the original callers
# (e.g., CNVkit, ControlFreeC)
if [ "$RUN_ORIGINAL" -gt "0" ]
then

# Prep the CNVkit data
Rscript --vanilla -e "rmarkdown::render('01-add-ploidy-cnvkit.Rmd', clean = TRUE)"

# Run annotation step for CNVkit WXS only
Rscript --vanilla 04-prepare-cn-file.R \
--cnv_file ${results_dir}/cnvkit_with_status.tsv \
--gtf_file $gtf_file \
--metadata $histologies_file \
--filename_lead "cnvkit_annotated_cn" \
--seg \
--runWXSonly

# Run annotation step for ControlFreeC tumor only
Rscript --vanilla 04-prepare-cn-file.R \
--cnv_file ${data_dir}/cnv-controlfreec-tumor-only.tsv.gz \
--gtf_file $gtf_file \
--metadata $histologies_file \
--filename_lead "freec-tumor-only_annotated_cn" \
--controlfreec

# Run merging for all annotated files
Rscript --vanilla 07-consensus-annotated-merge.R \
--cnvkit_auto ${results_dir}/cnvkit_annotated_cn_wxs_autosomes.tsv.gz \
--cnvkit_x_and_y ${results_dir}/cnvkit_annotated_cn_wxs_x_and_y.tsv.gz \
--consensus_auto ${results_dir}/consensus_seg_annotated_cn_autosomes.tsv.gz \
--consensus_x_and_y ${results_dir}/consensus_seg_annotated_cn_x_and_y.tsv.gz \
--cnv_tumor_auto ${results_dir}/freec-tumor-only_annotated_cn_autosomes.tsv.gz \
--cnv_tumor_x_and_y ${results_dir}/freec-tumor-only_annotated_cn_x_and_y.tsv.gz \
--outdir ${results_dir}

echo "prep CNVkit WXS data"
# Prep the CNVkit data
Rscript --vanilla -e "rmarkdown::render('01-add-ploidy-cnvkit.Rmd', clean = TRUE)"

echo "annotate CNVkit WXS CNVs"
# Run annotation step for CNVkit WXS only
Rscript --vanilla 04-prepare-cn-file.R \
--cnv_file ${results_dir}/cnvkit_with_status.tsv \
--gtf_file $gtf_file \
--metadata $histologies_file \
--filename_lead "cnvkit_annotated_cn" \
--seg \
--runWXSonly

echo "annotate FREEC WXS CNVs"
# Run annotation step for ControlFreeC
Rscript --vanilla 04-prepare-cn-file.R \
--cnv_file ${data_dir}/cnv-controlfreec.tsv.gz \
--gtf_file $gtf_file \
--metadata $histologies_file \
--filename_lead "controlfreec_annotated_cn" \
--controlfreec \
--runWXSonly

echo "annotate CNVkit tumor only CNVs"
# Run annotation step for ControlFreeC tumor only
Rscript --vanilla 04-prepare-cn-file.R \
--cnv_file ${data_dir}/cnv-controlfreec-tumor-only.tsv.gz \
--gtf_file $gtf_file \
--metadata $histologies_file \
--filename_lead "freec-tumor-only_annotated_cn" \
--controlfreec

results_dir=./results

echo "merge annotated files with cnvkit WXS"
# Run merging for all annotated files
Rscript --vanilla 07-consensus-annotated-merge.R \
--cnvkit_auto ${results_dir}/cnvkit_annotated_cn_wxs_autosomes.tsv.gz \
--cnvkit_x_and_y ${results_dir}/cnvkit_annotated_cn_wxs_x_and_y.tsv.gz \
--consensus_auto ${results_dir}/consensus_seg_annotated_cn_autosomes.tsv.gz \
--consensus_x_and_y ${results_dir}/consensus_seg_annotated_cn_x_and_y.tsv.gz \
--cnv_tumor_auto ${results_dir}/freec-tumor-only_annotated_cn_autosomes.tsv.gz \
--cnv_tumor_x_and_y ${results_dir}/freec-tumor-only_annotated_cn_x_and_y.tsv.gz \
--cnvkitWXS TRUE \
--outdir ${results_dir}

echo "merge annotated files with freec WXS"
# Run merging for all annotated files
Rscript --vanilla 07-consensus-annotated-merge.R \
--freec_auto ${results_dir}/controlfreec_annotated_cn_wxs_autosomes.tsv.gz \
--freec_x_and_y ${results_dir}/controlfreec_annotated_cn_wxs_x_and_y.tsv.gz \
--consensus_auto ${results_dir}/consensus_seg_annotated_cn_autosomes.tsv.gz \
--consensus_x_and_y ${results_dir}/consensus_seg_annotated_cn_x_and_y.tsv.gz \
--cnv_tumor_auto ${results_dir}/freec-tumor-only_annotated_cn_autosomes.tsv.gz \
--cnv_tumor_x_and_y ${results_dir}/freec-tumor-only_annotated_cn_x_and_y.tsv.gz \
--cnvkitWXS FALSE \
--outdir ${results_dir}

fi
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