[BUG-305] Handle VCF files - JIRA UNCC

Details

Type: Task
Status: Closed (View Workflow)
Priority: Minor
Resolution: Fixed
Labels:
None

Description

Add the ability to process .vcf files

Download BOTH attached files into same folder. Drag and drop the .vcf.gz (not the .vcf.gz.tbi). Make sure you can see it.

Attachments

Options
- Sort By Name
- Sort By Date
- Ascending
- Descending
- Thumbnails
- List
- Download All

Attachments

ALL.chr20.vqsr_2of5_union_200_sites_for_validation.20101123.indels.genotypes.vcf.gz
47 kB
09/Feb/12 10:41 AM
ALL.chr20.vqsr_2of5_union_200_sites_for_validation.20101123.indels.genotypes.vcf.gz.tbi
2 kB
09/Feb/12 10:41 AM

Issue Links

relates to

BUG-622 File format issues

Closed

Activity

Ascending order - Click to sort in descending order

Lance Frohman (Inactive) created issue - 25/Apr/11 10:15 AM

Lance Frohman (Inactive) made changes - 19/May/11 7:42 AM

Field	Original Value	New Value
Status	Open [ 1 ]	Resolved [ 5 ]
Resolution		Fixed [ 1 ]

Alyssa Gulledge (Inactive) made changes - 09/Feb/12 10:31 AM

Resolution	Fixed [ 1 ]
Status	Resolved [ 5 ]	Reopened [ 4 ]
Assignee	Lance Frohman [ lfrohman ]	Alyssa Gulledge [ alyssa ]

Alyssa Gulledge (Inactive) made changes - 09/Feb/12 10:41 AM

Attachment		ALL.chr20.vqsr_2of5_union_200_sites_for_validation.20101123.indels.genotypes.vcf.gz [ 10851 ]
Attachment		ALL.chr20.vqsr_2of5_union_200_sites_for_validation.20101123.indels.genotypes.vcf.gz.tbi [ 10852 ]
Description	Add the ability to process .vcf files - this will be dome as a separate bundle.	Add the ability to process .vcf files - this will be dome as a separate bundle. Add VCF handler plug in. Download BOTH attached files into same folder. Drag and drop the .vcf.gz (not the .vcf.gz.tbi). Make sure you can see it.

Alyssa Gulledge (Inactive) made changes - 09/Feb/12 10:41 AM

Status	Reopened [ 4 ]	Resolved [ 5 ]
Assignee	Alyssa Gulledge [ alyssa ]
Resolution		Fixed [ 1 ]

Alyssa Gulledge (Inactive) made changes - 09/Feb/12 10:41 AM

Status

Resolved [ 5 ]

Closed [ 6 ]

Alyssa Gulledge (Inactive) made changes - 09/Feb/12 10:41 AM

Project	Genentech [ 10034 ]	Bug Repository [ 10030 ]
Key	~~TODO-2~~	~~BUG-305~~

Fuquan Wang (Inactive) made changes - 06/Jun/12 10:04 AM

Resolution	Fixed [ 1 ]
Status	Closed [ 6 ]	Reopened [ 4 ]
Assignee		Fuquan Wang [ fwang4 ]

Hide

Permalink

Fuquan Wang (Inactive) added a comment - 08/Jun/12 11:21 AM

Failed - vcf file not supported in 7.0.0 (11845) Mac

Show

Fuquan Wang (Inactive) added a comment - 08/Jun/12 11:21 AM Failed - vcf file not supported in 7.0.0 (11845) Mac

Hide

Permalink

Lance Frohman (Inactive) added a comment - 08/Jun/12 11:24 AM

The VCFHandler plugin is not yet updated for IGB 7.0

Show

Lance Frohman (Inactive) added a comment - 08/Jun/12 11:24 AM The VCFHandler plugin is not yet updated for IGB 7.0

Fuquan Wang (Inactive) made changes - 11/Jun/12 7:06 AM

Assignee

Fuquan Wang [ fwang4 ]

Alyssa Gulledge [ alyssa ]

Hide

Permalink

Alyssa Gulledge (Inactive) added a comment - 11/Jun/12 8:53 AM

Lance, assign this back to me when the handler is updated and ready to be tested

Show

Alyssa Gulledge (Inactive) added a comment - 11/Jun/12 8:53 AM Lance, assign this back to me when the handler is updated and ready to be tested

Alyssa Gulledge (Inactive) made changes - 11/Jun/12 8:53 AM

Assignee

Alyssa Gulledge [ alyssa ]

Lance Frohman [ lfrohman ]

Hide

Permalink

Lance Frohman (Inactive) added a comment - 27/Jun/12 7:21 AM

VCF handler is ready (use Genentech development repository)

Show

Lance Frohman (Inactive) added a comment - 27/Jun/12 7:21 AM VCF handler is ready (use Genentech development repository)

Lance Frohman (Inactive) made changes - 27/Jun/12 7:21 AM

Assignee

Lance Frohman [ lfrohman ]

Alyssa Gulledge [ alyssa ]

Alyssa Gulledge (Inactive) made changes - 02/Jul/12 9:10 AM

Status	Reopened [ 4 ]	Resolved [ 5 ]
Assignee	Alyssa Gulledge [ alyssa ]
Resolution		Fixed [ 1 ]

Alyssa Gulledge (Inactive) made changes - 02/Jul/12 9:10 AM

Status

Resolved [ 5 ]

Closed [ 6 ]

Richard Linchangco (Inactive) made changes - 13/Nov/12 10:25 AM

Resolution	Fixed [ 1 ]
Status	Closed [ 6 ]	Reopened [ 4 ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 9:56 AM

Link

This issue relates to ~~BUG-622~~ [ ~~BUG-622~~ ]

Hide

Permalink

Alyssa Gulledge (Inactive) added a comment - 15/Nov/12 10:12 AM

VCF handler is now part of IGB main code - not a plug in any more.

Show

Alyssa Gulledge (Inactive) added a comment - 15/Nov/12 10:12 AM VCF handler is now part of IGB main code - not a plug in any more.

Hide

Permalink

Richard Linchangco (Inactive) added a comment - 28/Nov/12 8:50 AM

Passed V.13624, Mac, Java 1.06.0_37

As previously stated, VCF Handler has been integrated into IGB 7.0.0(13624) making this a LEGACY bug.

Show

Richard Linchangco (Inactive) added a comment - 28/Nov/12 8:50 AM Passed V.13624, Mac, Java 1.06.0_37 As previously stated, VCF Handler has been integrated into IGB 7.0.0(13624) making this a LEGACY bug.

Richard Linchangco (Inactive) made changes - 28/Nov/12 8:51 AM

Assignee

Alyssa Gulledge [ alyssa ]

Hide

Permalink

Alyssa Gulledge (Inactive) added a comment - 28/Nov/12 9:21 AM

Make sure that IGB can still properly parse and load and display the .vcf format files.

Show

Alyssa Gulledge (Inactive) added a comment - 28/Nov/12 9:21 AM Make sure that IGB can still properly parse and load and display the .vcf format files.

Alyssa Gulledge (Inactive) made changes - 28/Nov/12 9:21 AM

Assignee	Alyssa Gulledge [ alyssa ]	Richard Linchangco [ richard ]
Reporter	Lance Frohman [ lfrohman ]	Alyssa Gulledge [ alyssa ]
Description	Add the ability to process .vcf files - this will be dome as a separate bundle. Add VCF handler plug in. Download BOTH attached files into same folder. Drag and drop the .vcf.gz (not the .vcf.gz.tbi). Make sure you can see it.	Add the ability to process .vcf files Download BOTH attached files into same folder. Drag and drop the .vcf.gz (not the .vcf.gz.tbi). Make sure you can see it.

Hide

Permalink

Richard Linchangco (Inactive) added a comment - 28/Nov/12 9:29 AM

Passed V.13624, Mac, Java 1.06.0_37

Show

Richard Linchangco (Inactive) added a comment - 28/Nov/12 9:29 AM Passed V.13624, Mac, Java 1.06.0_37

Richard Linchangco (Inactive) made changes - 28/Nov/12 9:29 AM

Status	Reopened [ 4 ]	Resolved [ 5 ]
Assignee	Richard Linchangco [ richard ]	Alyssa Gulledge [ alyssa ]
Resolution		Fixed [ 1 ]

Alyssa Gulledge (Inactive) made changes - 28/Nov/12 11:01 AM

Resolution	Fixed [ 1 ]
Status	Resolved [ 5 ]	Reopened [ 4 ]
Assignee	Alyssa Gulledge [ alyssa ]

Richard Linchangco (Inactive) made changes - 28/Nov/12 12:27 PM

Status	Reopened [ 4 ]	Resolved [ 5 ]
Assignee		Alyssa Gulledge [ alyssa ]
Resolution		Fixed [ 1 ]

Alyssa Gulledge (Inactive) made changes - 04/Dec/12 8:26 AM

Assignee

Alyssa Gulledge [ alyssa ]

Alyssa Gulledge (Inactive) made changes - 04/Dec/12 8:28 AM

Status

Resolved [ 5 ]

Closed [ 6 ]

People

Assignee:

Unassigned

Reporter:

Alyssa Gulledge (Inactive)

Votes:

0 Vote for this issue

Watchers:

0 Start watching this issue

Dates

Created:

25/Apr/11 10:15 AM

Updated:

04/Dec/12 8:28 AM

Resolved:

28/Nov/12 12:27 PM