Tool for arrays QC metrics calculations #6812
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
kcibul
approved these changes
Sep 16, 2020
| "SELECT * FROM `" + genotypeCountsTable + "`"; | ||
|
|
||
| //Execute Query | ||
| final TableResult result = BigQueryUtils.executeQuery(genotypeCountQueryString); |
There was a problem hiding this comment.
Turns out that it's MUCH faster to use the storage API here (like 10-20 times) since you're pulling out the entire table. You can see what I do for this in the ArrayExtractCohort for probe_info
| thisRow.add(String.valueOf(excessHetPval)); | ||
|
|
||
| Double callRate = 1.0 - ((double) noCalls / sampleCount); | ||
| thisRow.add(String.valueOf(callRate)); |
There was a problem hiding this comment.
Do you want to format these to any kind of fixed precision? I know some of the GATK tools go to 3 decimal places. Same fo all the doubles
| Double excessHetPval = ExcessHet.calculateEH(genotypeCounts, sampleCount).getRight(); | ||
| thisRow.add(String.valueOf(excessHetPval)); | ||
|
|
||
| Double callRate = 1.0 - ((double) noCalls / sampleCount); |
There was a problem hiding this comment.
same for other types. If they can be null, use the object (Double) and be sure to handle the null case when you use them. if not use the primitive (double) and you don't have to worry!
meganshand
added a commit
that referenced
this pull request
Oct 6, 2020
kcibul
pushed a commit
that referenced
this pull request
Jan 29, 2021
kcibul
pushed a commit
that referenced
this pull request
Feb 1, 2021
Marianie-Simeon
pushed a commit
that referenced
this pull request
Feb 16, 2021
kcibul
pushed a commit
that referenced
this pull request
Mar 9, 2021
mmorgantaylor
pushed a commit
that referenced
this pull request
Apr 6, 2021
This was referenced Mar 17, 2023
Closed
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Pulls down a temp table of genotype counts, calculates excess het and call rate and writes them to a tsv for future upload.