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Intermediates and Filtering

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Keiran Raine edited this page Apr 14, 2021 · 5 revisions

After the initial group calling the BRASS flow progressively filters the groups down via several methods.

Some of the intermediate files are available in *.intermediates.tar.gz ordered as follows:

  1. .groups.gz - raw brass group output
  2. .groups.filtered.bedpe
  3. .groups.clean.bedpe

groups.gz

This is the raw output from the grouping algorithm:

  • cols 1-4 LOW chr, strand, start, stop
  • cols 5-8 HIGH chr, strand, start, stop
  • N columns of read counts from each sample (see #NSAMPLES in header) ordered as per the header
  • Hits repeat (. unless repeat filtering was used)
  • N columns of read NAMES from each sample (see #NSAMPLES in header) ordered as per the header

intermediates.tar.gz - complete listing

$ tar -ztf $SAMPLE.brass.intermediates.tar.gz 
intermediates/
intermediates/$SAMPLE_vs_$CONTROL.r5
intermediates/$SAMPLE.insert_size_distr
intermediates/$SAMPLE_vs_$CONTROL.r6
intermediates/$SAMPLE_vs_$CONTROL.inversions.pdf
intermediates/$SAMPLE_vs_$CONTROL.r5.scores
intermediates/samp_stats.txt
intermediates/$SAMPLE.ngscn.fb_reads.bed.gz
intermediates/$SAMPLE_vs_$CONTROL.r2
intermediates/$SAMPLE_vs_$CONTROL.groups.filtered.bedpe
intermediates/$SAMPLE_vs_$CONTROL.r4
intermediates/$SAMPLE_vs_$CONTROL.groups.gz
intermediates/$SAMPLE_vs_$CONTROL.r3
intermediates/$SAMPLE_vs_$CONTROL.cn_filtered
intermediates/$SAMPLE_vs_$CONTROL.ngscn.abs_cn.bg.gz
intermediates/$CONTROL.ngscn.fb_reads.bed.gz
intermediates/$SAMPLE.ngscn.bed.gz
intermediates/$CONTROL.ngscn.bed.gz
intermediates/$SAMPLE_vs_$CONTROL.ngscn.abs_cn.bg.rg_cns.gz
intermediates/$SAMPLE_vs_$CONTROL.is_fb_artefact.txt
intermediates/$SAMPLE_vs_$CONTROL.ngscn.segments.abs_cn.bg.gz
intermediates/$SAMPLE_vs_$CONTROL.groups.clean.bedpe
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