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Include neutral changes in cnv consensus .seg file #476
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Removing `src` directory to unnest `scripts` and adding `ref` directory for genomic info files.
Link and script to process downloaded file for segmental duplciations.
These regions are the ones defined by @hongboxie here: AlexsLemonade#438 (comment) Converted from hg18 to hg38
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.
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
we don't need data types here, so keeping everything as strings simplifies, and removes potential errors from unexpected conversions from int to float
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Put all intermediate files in a defined scratch sub directory.
jaclyn-taroni
approved these changes
Jan 27, 2020
| @@ -52,6 +52,8 @@ def remove_dup_null_outside(cell, start, end): | |||
| ) | |||
| parser.add_argument('--file', required=True, | |||
| help='path to the file that needs duplicates and NULLs removed') | |||
| parser.add_argument('--uncalled', required=False, | |||
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No it is not. I had thoughts that I might use it to annotate where there were only two possible callers, but abandoned that plan on some reflection. I'll remove it unless there is some great idea for how to use the information in this step.
Co-Authored-By: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
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Purpose/implementation Section
What scientific question is your analysis addressing?
GISTIC requires all assayed regions to be included for every sample, so the previous version of
pbta-cnv-consensus.segwas failing to run. This set of changes is to update the creation of that file to include the full set of "neutral" changes (copy number 2) in the seg file.What was your approach?
Many regions of the genome are excluded from CN calls in the consensus script, so it does not make sense to simply complement the CNV consensus calls to find the neutral regions. Instead, I first created a file of "callable" regions by removing any large segments that were excluded in the CNV consensus calling pipeline, such as telomeres, centromeres, and segmental duplications.
In addition, samples that were filtered out due to high numbers of segment calls are not included in the final .seg file.
What GitHub issue does your pull request address?
#392
#453
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Which areas should receive a particularly close look?
Is the process for generating the callable regions reasonable? The size cutoff of 200kb was selected somewhat arbitrarily, with the goal of not creating too many separate segments, as some downstream analysis will filter samples based on segment number, even if most of those segments have copy number 2.
I currently exclude samples where only one caller passed filters, as those can not by definition have any consensus calls (2 callers must agree). However, the samples with only two callers (where one was excluded) are likely to have a different error profile (and probably fewer net calls). Is this something we should flag, and if so how? There does not seem to be much in the way of tumor type bias in this set, which is good.
Is there anything that you want to discuss further?
Some of the changes here depend on file name changes in #467, so that PR should probably be merged in before this one.
Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?
Results
What types of results are included (e.g., table, figure)?
What is your summary of the results?
Reproducibility Checklist
Documentation Checklist
READMEand it is up to date.analyses/README.mdand the entry is up to date.