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Reproducing copy number excluded regions #438
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From @xiehongbo via email:
Using hg18->hg38 liftover, these correspond to: Which are the regions as found in the provided file. I will update the analysis to include this as a starting point. |
jashapiro
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These regions are the ones defined by @hongboxie here: AlexsLemonade#438 (comment) Converted from hg18 to hg38
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* add to Snakefile * updating fork * changed output path and name * implement segmean * implement segmean * add result file * add result files * add trailing line * fix .py * change Snakefile comment * change README.md * change README.md * Updates to file organization Removing `src` directory to unnest `scripts` and adding `ref` directory for genomic info files. * add alternative segdup generation Link and script to process downloaded file for segmental duplciations. * Updates to blacklist generation * Add IG regions These regions are the ones defined by @hongboxie here: #438 (comment) Converted from hg18 to hg38 * Add step to potentially fix overlapping dup del segments. * Notebook to look at consensus calls for overlaps * Add overlap pruning * Update output files Note that ordering has changed, but the actual differences between these files should be relatively small other than that. There are changes to the cnv_consensus.tsv file where segments that are not contained within the defined CNV are discarded but might have been retained before. * update readme * Add telomere definition file * Update blacklist generation script * Remove accidentally included notebook * Tried to clarify complicated bedtools step. * Update analyses/copy_number_consensus_call/scripts/remove_dup_NULL_overlap_entries.py Co-Authored-By: Candace Savonen <cansav09@gmail.com> * Update analyses/copy_number_consensus_call/scripts/remove_dup_NULL_overlap_entries.py Co-Authored-By: Candace Savonen <cansav09@gmail.com> * Add more clarifying comments * Add full exclusion list and remove outdated files * Update readmes * Updated output files. * Re-add previous blacklist * More descriptive excluded file name * Update filename Co-authored-by: Candace Savonen <cansav09@gmail.com> Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
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* add to Snakefile * updating fork * changed output path and name * implement segmean * implement segmean * add result file * add result files * add trailing line * fix .py * change Snakefile comment * change README.md * change README.md * Updates to file organization Removing `src` directory to unnest `scripts` and adding `ref` directory for genomic info files. * add alternative segdup generation Link and script to process downloaded file for segmental duplciations. * Updates to blacklist generation * Add IG regions These regions are the ones defined by @hongboxie here: #438 (comment) Converted from hg18 to hg38 * Add step to potentially fix overlapping dup del segments. * Notebook to look at consensus calls for overlaps * Add overlap pruning * Update output files Note that ordering has changed, but the actual differences between these files should be relatively small other than that. There are changes to the cnv_consensus.tsv file where segments that are not contained within the defined CNV are discarded but might have been retained before. * update readme * Add telomere definition file * Update blacklist generation script * Remove accidentally included notebook * Tried to clarify complicated bedtools step. * Update analyses/copy_number_consensus_call/scripts/remove_dup_NULL_overlap_entries.py Co-Authored-By: Candace Savonen <cansav09@gmail.com> * Update analyses/copy_number_consensus_call/scripts/remove_dup_NULL_overlap_entries.py Co-Authored-By: Candace Savonen <cansav09@gmail.com> * Add more clarifying comments * Add full exclusion list and remove outdated files * Update readmes * Updated output files. * Re-add previous blacklist * Add chromosome lengths file * Create file of neutral regions * Use hg.38.chrom.sizes * More descriptive excluded file name * Update filename * Sort chromosomes and remove alt from callable. * Fix sed command * Finish the rule to combine neutral regions. * Add output of bad callers * Bad caller summary notebook * Add output of neutral segments to the seg file Neutral segments (copy number 2) are included if they fall within a "callable region" which is one not covered by a large excluded region. When we add these back, we still exclude specimens where more than two callers 'failed' with high numbers of segments * remove working notebooks * Bug fixes * Unset X and Y copy number calls * Update README * Add callable regions to analyses/README.md * Simplify output file description in readme * Simplify file reading we don't need data types here, so keeping everything as strings simplifies, and removes potential errors from unexpected conversions from int to float * comment out status message * Move segfile step into snakemake * Fix filename in snakemake * Update results. * Update scratch dir handling Put all intermediate files in a defined scratch sub directory. * Update analyses/copy_number_consensus_call/scripts/bed_to_segfile.R Co-Authored-By: Jaclyn Taroni <jaclyn.n.taroni@gmail.com> * remove unused option. Co-authored-by: Candace Savonen <cansav09@gmail.com> Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
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What data file(s) does this issue pertain to?
https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/master/analyses/copy_number_consensus_call/src/scripts/IGLL_telo_centromeric_region.txt
Put your question or report your issue here.
I am trying to reproduce the generation of the
IGLL_telo_centromeric_region.txtfile that is used for Copy number consensus generation #128. This file includes regions that are to be excluded from analysis due to high error rates. The telomeres and centromeres can be reproduced from UCSC data files, but I am confused by the immunoglobulin regions. The documentation points to http://penncnv.openbioinformatics.org/en/latest/misc/faq/, but it is not clear from where the enumerations of those regions is defined. Moreover, the regions defined there are for hg18:However, the regions in the
IGLL_telo_centromeric_region.txtfile do not seem to correspond to a liftOver of those regions to hg38Applying liftOver hg18->hg38, I get the following regions:
The nearest equivalent regions in
IGLL_telo_centromeric_region.txtseem to be these:(There are only three here, presumably because the other chr14 region falls near a telomere and is excluded that way?)
In addition,
IGLL_telo_centromeric_region.txtincludes the regionchr21:3100000-7000000which is listed as astalk(acrocentric arm) the UCSC cytoband file, but no otherstalkregions are excluded, so I was not sure why this one was.Can @fingerfen or @xiehongbo provide some additional information?
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