Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

#260 filter out AS_QD, SOR, FS from cohort extract VCF #7173

Merged
merged 3 commits into from
Apr 2, 2021
Merged

#260 filter out AS_QD, SOR, FS from cohort extract VCF #7173

merged 3 commits into from
Apr 2, 2021

Conversation

schaluva
Copy link

No description provided.

@gatk-bot
Copy link

gatk-bot commented Mar 30, 2021 •
edited
Loading

Travis reported job failures from build 33415
Failures in the following jobs:

Test Type JDK Job ID Logs
cloud openjdk11 33415.14 logs
cloud openjdk8 33415.1 logs

@gatk-bot
Copy link

gatk-bot commented Mar 30, 2021 •
edited
Loading

Travis reported job failures from build 33418
Failures in the following jobs:

Test Type JDK Job ID Logs
cloud openjdk8 33418.1 logs
cloud openjdk11 33418.14 logs

kcibul
kcibul approved these changes Apr 2, 2021
View reviewed changes
Copy link
Contributor

@kcibul kcibul left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

lgtm

src/main/java/org/broadinstitute/hellbender/tools/variantdb/CommonCode.java Outdated
@@ -145,13 +145,13 @@ public static VCFHeader generateVcfHeader(Set<String> sampleNames,//) { //final
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.VARIANT_DEPTH_KEY));

headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_STRAND_ODDS_RATIO_KEY));
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.STRAND_ODDS_RATIO_KEY));
// headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.STRAND_ODDS_RATIO_KEY));
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

delete

src/main/java/org/broadinstitute/hellbender/tools/variantdb/CommonCode.java Outdated

headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_FISHER_STRAND_KEY));
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.FISHER_STRAND_KEY));
// headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.FISHER_STRAND_KEY));
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

delete

src/main/java/org/broadinstitute/hellbender/tools/variantdb/CommonCode.java Outdated


headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_QUAL_BY_DEPTH_KEY));
// headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_QUAL_BY_DEPTH_KEY));
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

delete

@schaluva schaluva merged commit 38675fd into ah_var_store Apr 2, 2021
@schaluva schaluva deleted the filter_annotations branch April 2, 2021 16:22
mmorgantaylor pushed a commit that referenced this pull request Apr 6, 2021
@schaluva @mmorgantaylor
#260 filter out AS_QD, SOR, FS from cohort extract VCF (#7173)
c30dd54 
* filter out AS_QD, SOR, FS from cohort extract VCF

* change files to original and expected

* delete commented out lines
This was referenced Mar 17, 2023
Closed
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@kcibul kcibul kcibul approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@schaluva @gatk-bot @kcibul