It looks like this is the only mention of PGT in docs #6221
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
droazen
approved these changes
Oct 18, 2019
| @@ -113,7 +113,7 @@ public static VCFFormatHeaderLine getEquivalentFormatHeaderLine(final String inf | |||
| addFormatLine(new VCFFormatHeaderLine(MLE_PER_SAMPLE_ALLELE_FRACTION_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Maximum likelihood expectation (MLE) for the alternate allele fraction, in the same order as listed, for each individual sample")); | |||
| addFormatLine(new VCFFormatHeaderLine(PL_FOR_ALL_SNP_ALLELES_KEY, 10, VCFHeaderLineType.Integer, "Phred-scaled genotype likelihoods for all 4 possible bases regardless of whether there is statistical evidence for them. Ordering is always PL for AA AC CC GA GC GG TA TC TG TT.")); | |||
| addFormatLine(new VCFFormatHeaderLine(HAPLOTYPE_CALLER_PHASING_ID_KEY, 1, VCFHeaderLineType.String, "Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group")); | |||
| addFormatLine(new VCFFormatHeaderLine(HAPLOTYPE_CALLER_PHASING_GT_KEY, 1, VCFHeaderLineType.String, "Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another")); | |||
| addFormatLine(new VCFFormatHeaderLine(HAPLOTYPE_CALLER_PHASING_GT_KEY, 1, VCFHeaderLineType.String, "Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozgyous and is not intended to describe called alleles")); | |||
There was a problem hiding this comment.
heterozgyous -> heterozygous
There was a problem hiding this comment.
I can't even get a one-line PR right.
There was a problem hiding this comment.
It's my fault @ldgauthier for claiming that it would be a one-line PR. I forgot that the HaplotypeCaller exact-match tests would fail due to the header differences (https://storage.googleapis.com/hellbender-test-logs/build_reports/master_27820.4/tests/test/index.html). The good news is that these days we have that UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS boolean you can turn on in HaplotypeCallerIntegrationTest to auto-update the offending files.
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.
No description provided.