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the file "merge_vcfwide_stat_shards.merged_vcf_stats"? #17

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jingydz opened this issue Oct 9, 2023 · 0 comments
Open

the file "merge_vcfwide_stat_shards.merged_vcf_stats"? #17

jingydz opened this issue Oct 9, 2023 · 0 comments

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@jingydz
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jingydz commented Oct 9, 2023 •
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vcfstats=merge_vcfwide_stat_shards.merged_vcf_stats,

command <<<
# Plot VCF-wide distributions
/opt/sv-pipeline/scripts/vcf_qc/plot_sv_vcf_distribs.R
-N $( cat \${samples_list} | sort | uniq | wc -l )
-S /opt/sv-pipeline/ref/vcf_qc_refs/SV_colors.txt
${vcfstats}
plotQC_vcfwide_output/

# Prep outputs
tar -czvf ${prefix}.plotQC_vcfwide_output.tar.gz
plotQC_vcfwide_output

output {
File plots_tarball = "${prefix}.plotQC_vcfwide_output.tar.gz"
}

I want to plot the SV distribution, but I am wonder the vcfstats file?
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@jingydz