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Inconsistent ROC reporting compared to labeled VCF #87

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ksw9 opened this issue Jun 20, 2019 · 0 comments
Open

Inconsistent ROC reporting compared to labeled VCF #87

ksw9 opened this issue Jun 20, 2019 · 0 comments

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@ksw9
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ksw9 commented Jun 20, 2019

Hi,
I have used hap.py to measure performance and get a strange result in which at the highest value of my QQ field (QUAL = 228), a very low recall of 0.018067 is reported. This is incorrect when I examine the labeled VCF with TP and FPs, where true recall should be 0.9430894 (1044/1107).

I run hap.py with the following command:
hap.py -r ${ref} $truth $query -o ${output} --set-gt hom --roc QUAL

Any suggestions would be wonderful. Thank you!

# ROC for highest QUAL value
SNP,*,*,ALL,*,QUAL,228.000000,0.018067,0.384615,0.0,0.034513,0,0,4411532,,0.000000,1107,651.000000,456.000000,.,.,1.4276315789473684,,20,10.000000,10.000000,.,.,1.0,,1087,641.000000,446.000000,.,.,1.437219730941704,,52,23.000000,28.000000,.,.,0.8214285714285714,,20,10.000000,10.000000,.,.,1.0,,32,13.000000,18.000000,.,.,0.7222222222222222,,0,0.000000,0.000000,.,.,,
dskola pushed a commit that referenced this issue Oct 11, 2019
@Kentalot
Update RELEASES.md (#87)
d4d6219
dskola pushed a commit that referenced this issue Oct 11, 2019
Documentation updates for 0.3.12 release (#110)
a0e134d 
* Update RELEASES.md (#87)

* Updated RELASES.md and normalization.md (#109)
dskola pushed a commit that referenced this issue Oct 11, 2019
Merge doc changes from dev (#112)
ef5e1b4 
* Update RELEASES.md (#87)

* Updated RELASES.md and normalization.md (#109)

* Update more docs (#111)

* Update happy.md

* Cleaned up normalisation.md

* Update happy.md

* Created a new section for working with genome VCFs
  * Added description of --filter-nonref
  * Updated description of --convert-gvcf-xxxx options
  * Added note toward beginning of document calling attention to genome VCF section
* Fixed broken links in TOC
* Fixed inconsistent case in headings
dskola pushed a commit that referenced this issue Oct 11, 2019
Remove tag (#113)
6542350 
* Documentation updates for 0.3.12 release (#110)

* Update RELEASES.md (#87)

* Updated RELASES.md and normalization.md (#109)

* Merge doc changes from dev (#112)

* Update RELEASES.md (#87)

* Updated RELASES.md and normalization.md (#109)

* Update more docs (#111)

* Update happy.md

* Cleaned up normalisation.md

* Update happy.md

* Created a new section for working with genome VCFs
  * Added description of --filter-nonref
  * Updated description of --convert-gvcf-xxxx options
  * Added note toward beginning of document calling attention to genome VCF section
* Fixed broken links in TOC
* Fixed inconsistent case in headings
dskola pushed a commit that referenced this issue Oct 11, 2019
Clean merge (#115)
f0a76a5 
* fix bold GFM rendering

Without a space between the *** and the : , Github won't render *** as bold.

* typos?

* Clarify that INFO.VQSLOD is required for --roc

* Update read me with GCC/G++ 4.9.2+ requirement

See #66

* Remove regex dependency + fix test error with gcc 7.3

* Fix Docker build

* Update rtg-tools to work with new Java

* Documentation updates for 0.3.12 release (#110)

* Update RELEASES.md (#87)

* Updated RELASES.md and normalization.md (#109)

* Merge doc changes from dev (#112)

* Update RELEASES.md (#87)

* Updated RELASES.md and normalization.md (#109)

* Update more docs (#111)

* Update happy.md

* Cleaned up normalisation.md

* Update happy.md

* Created a new section for working with genome VCFs
  * Added description of --filter-nonref
  * Updated description of --convert-gvcf-xxxx options
  * Added note toward beginning of document calling attention to genome VCF section
* Fixed broken links in TOC
* Fixed inconsistent case in headings

* Resolved merge conflict

* Remove seemingly-unused ENV command

* Restore ENV DEBIAN_FRONTEND=noninteractive
dskola pushed a commit that referenced this issue Oct 11, 2019
Merge all (#116)
eb9d746 
* fix bold GFM rendering

Without a space between the *** and the : , Github won't render *** as bold.

* typos?

* Clarify that INFO.VQSLOD is required for --roc

* Update read me with GCC/G++ 4.9.2+ requirement

See #66

* Remove regex dependency + fix test error with gcc 7.3

* Fix Docker build

* Update rtg-tools to work with new Java

* Updated RELASES.md and normalization.md (#109)

* Documentation updates for 0.3.12 release (#110)

* Update RELEASES.md (#87)

* Updated RELASES.md and normalization.md (#109)

* Update more docs (#111)

* Update happy.md

* Cleaned up normalisation.md

* Update happy.md

* Created a new section for working with genome VCFs
  * Added description of --filter-nonref
  * Updated description of --convert-gvcf-xxxx options
  * Added note toward beginning of document calling attention to genome VCF section
* Fixed broken links in TOC
* Fixed inconsistent case in headings

* Merge doc changes from dev (#112)

* Update RELEASES.md (#87)

* Updated RELASES.md and normalization.md (#109)

* Update more docs (#111)

* Update happy.md

* Cleaned up normalisation.md

* Update happy.md

* Created a new section for working with genome VCFs
  * Added description of --filter-nonref
  * Updated description of --convert-gvcf-xxxx options
  * Added note toward beginning of document calling attention to genome VCF section
* Fixed broken links in TOC
* Fixed inconsistent case in headings

* Remove tag (#113)

* Documentation updates for 0.3.12 release (#110)

* Update RELEASES.md (#87)

* Updated RELASES.md and normalization.md (#109)

* Merge doc changes from dev (#112)

* Update RELEASES.md (#87)

* Updated RELASES.md and normalization.md (#109)

* Update more docs (#111)

* Update happy.md

* Cleaned up normalisation.md

* Update happy.md

* Created a new section for working with genome VCFs
  * Added description of --filter-nonref
  * Updated description of --convert-gvcf-xxxx options
  * Added note toward beginning of document calling attention to genome VCF section
* Fixed broken links in TOC
* Fixed inconsistent case in headings

* Resolved merge conflict

* Remove seemingly-unused ENV command

* Restore ENV DEBIAN_FRONTEND=noninteractive
dskola pushed a commit that referenced this issue Oct 11, 2019
Dev (#117)
ef84473 
* Updated RELASES.md and normalization.md (#109)

* Update more docs (#111)

* Update happy.md

* Cleaned up normalisation.md

* Update happy.md

* Created a new section for working with genome VCFs
  * Added description of --filter-nonref
  * Updated description of --convert-gvcf-xxxx options
  * Added note toward beginning of document calling attention to genome VCF section
* Fixed broken links in TOC
* Fixed inconsistent case in headings

* Remove tag (#113)

* Documentation updates for 0.3.12 release (#110)

* Update RELEASES.md (#87)

* Updated RELASES.md and normalization.md (#109)

* Merge doc changes from dev (#112)

* Update RELEASES.md (#87)

* Updated RELASES.md and normalization.md (#109)

* Update more docs (#111)

* Update happy.md

* Cleaned up normalisation.md

* Update happy.md

* Created a new section for working with genome VCFs
  * Added description of --filter-nonref
  * Updated description of --convert-gvcf-xxxx options
  * Added note toward beginning of document calling attention to genome VCF section
* Fixed broken links in TOC
* Fixed inconsistent case in headings

* Clean merge (#115)

* fix bold GFM rendering

Without a space between the *** and the : , Github won't render *** as bold.

* typos?

* Clarify that INFO.VQSLOD is required for --roc

* Update read me with GCC/G++ 4.9.2+ requirement

See #66

* Remove regex dependency + fix test error with gcc 7.3

* Fix Docker build

* Update rtg-tools to work with new Java

* Documentation updates for 0.3.12 release (#110)

* Update RELEASES.md (#87)

* Updated RELASES.md and normalization.md (#109)

* Merge doc changes from dev (#112)

* Update RELEASES.md (#87)

* Updated RELASES.md and normalization.md (#109)

* Update more docs (#111)

* Update happy.md

* Cleaned up normalisation.md

* Update happy.md

* Created a new section for working with genome VCFs
  * Added description of --filter-nonref
  * Updated description of --convert-gvcf-xxxx options
  * Added note toward beginning of document calling attention to genome VCF section
* Fixed broken links in TOC
* Fixed inconsistent case in headings

* Resolved merge conflict

* Remove seemingly-unused ENV command

* Restore ENV DEBIAN_FRONTEND=noninteractive
dskola pushed a commit that referenced this issue Oct 11, 2019
master->sandbox (#118)
89e0f5b 
* Documentation updates for 0.3.12 release (#110)

* Update RELEASES.md (#87)

* Updated RELASES.md and normalization.md (#109)

* Merge doc changes from dev (#112)

* Update RELEASES.md (#87)

* Updated RELASES.md and normalization.md (#109)

* Update more docs (#111)

* Update happy.md

* Cleaned up normalisation.md

* Update happy.md

* Created a new section for working with genome VCFs
  * Added description of --filter-nonref
  * Updated description of --convert-gvcf-xxxx options
  * Added note toward beginning of document calling attention to genome VCF section
* Fixed broken links in TOC
* Fixed inconsistent case in headings

* Fix unmergable typo directly in master (#119)

This little space has caused no end of problems in getting these branches synced up. I'm hopeful that attacking it directly at the source may relieve the issues.
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