The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Get notifications!


You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

Did you remember to?


1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

Did we ask for a bug report?


Then follow instructions in Article#1894.

Formatting tip!


Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.

Jump to another community
Picard 2.9.0 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

CombineVariants --removeFILTER feature request

tommycarstensentommycarstensen United KingdomMember Posts: 404 ✭✭✭

When using CombineVariants, my variants get a FILTER value of either PASS or LowQual. Would it be possible to add an option to CombineVariants which prevents the FILTER value to be set to PASS? Otherwise I have to do some file processing before I run ApplyRecalibration further downstream. It would be great if this was a feature of all walkers and not just VariantFiltration. I'm not sure if the forum is the right place for feature requests. Happy to use Bugzilla or similar instead. Thanks.

Best Answer

  • ebanksebanks Broad InstituteMember, Broadie, Dev Posts: 692 ✭✭✭
    Accepted Answer

    Ah, now I understand. Okay, I'll log a report for this. It's not a high priority item obviously but we'll try to fix it before the next release. Thanks!

    Eric Banks, PhD -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT

Answers

  • ebanksebanks Broad InstituteMember, Broadie, Dev Posts: 692 ✭✭✭

    Hi Tommy,

    I'm a bit confused - why do you need to do processing before Apply Recalibration to handle PASSing filter fields? Are you saying that it's incorrectly turning filtered records ("LowQual") into PASSing ones?

    Eric Banks, PhD -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT

  • tommycarstensentommycarstensen United KingdomMember Posts: 404 ✭✭✭

    Hi Eric,

    LowQual sites are not turned into PASSed sites; at least I haven't seen it for the few entries I checked.

    Here is what happens. CombineVariants writes the FILTER value PASS to SNPs and INDELs. ApplyRecalibration will not modify/update the FILTER value of INDELs when VQSR is run on SNPs and vice versa. It's confusing if you look at the AR VCF output. I couldn't understand, why my INDELs were PASSed. It's not a big problem in my case though, because ProduceBeagleInput follows AR in my case and PBI only emits SNPs anyway. In the meantime I ended up writing my own tool to replace the functionalities of ApplyRecalibration and ProduceBeagleInput to save looping over the same data twice and saving the same data to disk twice.

    Thanks and sorry for posting my request. If I had known it was only INDELs left as PASSed, then I wouldn't have asked for the feature. Thanks.

  • ebanksebanks Broad InstituteMember, Broadie, Dev Posts: 692 ✭✭✭

    Sorry for being thick here, but I still don't actually understand the problem. What is it exactly that isn't working with PASS in the FILTER field? Thanks.

    Eric Banks, PhD -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT

  • tommycarstensentommycarstensen United KingdomMember Posts: 404 ✭✭✭

    Hi Eric,

    I didn't explain very well.

    After CombineVariants I have this INDEL:
    1 10106 . C CA 682.56 PASS

    After ApplyRecalibration --mode SNP I have this INDEL:
    1 10106 . C CA 682.56 PASS

    The INDEL obviously didn't PASS the VQSR filtering step run on SNPs, but rather the FILTER field is a remnant of running CombineVariants. It just confused me, when I saw it. It's not a problem for my downstream analysis.

    Thanks.

  • ebanksebanks Broad InstituteMember, Broadie, Dev Posts: 692 ✭✭✭
    Accepted Answer

    Ah, now I understand. Okay, I'll log a report for this. It's not a high priority item obviously but we'll try to fix it before the next release. Thanks!

    Eric Banks, PhD -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT

Sign In or Register to comment.