Slice VCF not retaining INFO data

Question: Slice VCF not retaining INFO data

4.0 years ago by

Mark Crowe • 100

QFAB, Brisbane

Mark Crowe • 100 wrote:

Hi folks

I'm using the Slice VCF tools to extract variants from a .vcf file that fall within regions defined by a .bed file. But I'm finding that all the INFO data from the initial vcf is being lost - the output file has just a '.' for each line in the INFO column. All other column data are retained after the filtering. Has anyone else come across this and found a way of keeping that data in the output? Thanks.

Cheers

Mark

snp vcf • 1.2k views

ADD COMMENT • link •

modified 3.7 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.0 years ago by Mark Crowe • 100

3.7 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi Mark,

Is this still a problem with the latest version of the tool? If so, a Trello ticket should be opened to report the issue, if that has not been done already (I didn't see one).
http://wiki.galaxyproject.org/Issues

If you want to share a history with an example so we can double check your specific data/job (and eliminate other issues), we can look at that, too. Send the share link from Main to the list galaxy-bugs at galaxyproject dot org and include a link to this post.

Thanks, Jen, Galaxy team

ADD COMMENT • link written 3.7 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen

I've just re-run it, and it seems that it's still stripping INFO data. I'll log on Trello and send through a history link to the bug mailing list for you.

Cheers

Mark

ADD REPLY • link written 3.7 years ago by Mark Crowe • 100

Hi Jen

I've tried logging a bug report to the galaxy-bugs mailing list and am getting an error that it doesn't exist "The e-mail address you entered couldn't be found". Is that the correct address please?

Cheers

Mark

From: Jennifer Hillman Jackson on Galaxy Biostar <notifications@biostars.org<mailto:notifications@biostars.org>> Reply-To: "galaxystar+0b21b15a+code@biostars.io<mailto:galaxystar+0b21b15a+code@biostars.io>" <galaxystar+0b21b15a+code@biostars.io<mailto:galaxystar+0b21b15a+code@biostars.io>> Date: Tuesday, 24 March 2015 2:48 To: Mark Louis Crowe <m.crowe@qfab.org<mailto:m.crowe@qfab.org>> Subject: [galaxy-biostar] A: Slice VCF not retaining INFO data

Activity on a post you are following on Galaxy Biostar<http: biostar.usegalaxy.org="">

User Jennifer Hillman Jackson<http: biostar.usegalaxy.org="" u="" 254=""/> wrote Answer: Slice VCF not retaining INFO data<http: biostar.usegalaxy.org="" p="" 9661="" #11335="">:

Hi Mark,

Thanks, Jen, Galaxy team

ADD REPLY • link written 3.7 years ago by Mark Crowe • 100

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