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Welcome for the RTG Users group. This group provides a facility for users to initiate discussions and questions about RTG products for analysis of High Throughput Sequencing data. Posts from new members are moderated to prevent spam, so don't panic if your message doesn't turn up immediately.

There is a separate group for announcements of new software releases at https://groups.google.com/a/realtimegenomics.com/forum/#!forum/rtg-announce

Support questions may also be directed by email to support@realtimegenomics.com

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Laura mora, Len Trigg3

May 29

vcfeval+hap.py qfy.py FP output

Thanks for the clarification Len! On Wednesday, 28 May 2025 at 23:24:24 UTC+2 Len Trigg wrote: Hi

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vcfeval+hap.py qfy.py FP output

Thanks for the clarification Len! On Wednesday, 28 May 2025 at 23:24:24 UTC+2 Len Trigg wrote: Hi

May 29

Dayzu Quinto, Sean Irvine2

12/19/24

error when merging two VCFs

Hi Dayzu, That looks like the process was killed by the operating system, most likely because you ran

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error when merging two VCFs

Hi Dayzu, That looks like the process was killed by the operating system, most likely because you ran

12/19/24

8/5/24

Haplotype-aware trio analysis

Hi all, I was hoping to try out using `rtg mendelian` to do some trio analysis, and was wondering to

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Haplotype-aware trio analysis

Hi all, I was hoping to try out using `rtg mendelian` to do some trio analysis, and was wondering to

8/5/24

Sai, Len Trigg3

5/21/24

Error while merging trio VCFs

Thanks, Len! On Sunday, May 19, 2024 at 11:26:11 PM UTC-5 Len Trigg wrote: On Mon, 20 May 2024 at 09:

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Error while merging trio VCFs

Thanks, Len! On Sunday, May 19, 2024 at 11:26:11 PM UTC-5 Len Trigg wrote: On Mon, 20 May 2024 at 09:

5/21/24

Marta Baragli, Sean Irvine2

5/3/24

allele ID out of range

Hi Marta, You are correct, the problem is that the record is referring to an alternate (ALT) allele

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allele ID out of range

Hi Marta, You are correct, the problem is that the record is referring to an alternate (ALT) allele

5/3/24

Glenn Carson, Len Trigg2

3/20/24

vcfeval --roc-subset behavior

Hi Glenn, Yes, you should be able to use --roc-expr to do what you want. It also turns out that we

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vcfeval --roc-subset behavior

Hi Glenn, Yes, you should be able to use --roc-expr to do what you want. It also turns out that we

3/20/24

Yee Man Chan, Len Trigg3

2/14/24

Misclassification when a deletion overlaps snp?

Thanks Len for the detailed reply. I tried to change the vcfs per your instruction as follows: truth.

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Misclassification when a deletion overlaps snp?

Thanks Len for the detailed reply. I tried to change the vcfs per your instruction as follows: truth.

2/14/24

Luka Topalovic, Sean Irvine2

10/15/23

Understanding TPC>TPB

Hi Luka, The simple answer is that callers can represent variants differently and there is not

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Understanding TPC>TPB

Hi Luka, The simple answer is that callers can represent variants differently and there is not

10/15/23

Alexandra Vatsiou, Len Trigg2

8/15/23

Hi Alexandra, Can you send through a small example VCF and the command line you are using that

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Hi Alexandra, Can you send through a small example VCF and the command line you are using that

8/15/23

Charles Warden, Len Trigg3

8/15/23

vcfeval: Error: An IO problem occurred: "Expected file missing"

Hi Len, Thank you very much for your prompt response. I was using a .sdf file/folder downloaded from

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vcfeval: Error: An IO problem occurred: "Expected file missing"

Hi Len, Thank you very much for your prompt response. I was using a .sdf file/folder downloaded from

8/15/23

huyen nguyen, Len Trigg2

8/9/23

error on operating system

Are you on a newer macbook? If so, comment out the "pre-flight safety checks" lines 4-12 of

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error on operating system

Are you on a newer macbook? If so, comment out the "pre-flight safety checks" lines 4-12 of

8/9/23

Len Trigg, Peter Pruisscher2

7/7/23

Re: [rtg-users] RTG output on exomes

Hi Len, Thank you for the explanation, this also how I will move forward. Have a good summer! Best,

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Re: [rtg-users] RTG output on exomes

Hi Len, Thank you for the explanation, this also how I will move forward. Have a good summer! Best,

7/7/23

Asher Bryant, Sean Irvine2

7/4/23

true positives classified as false negatives by bndeval

Hi Asher, I hope I have interpreted your question correctly, but I believe the problem is that the

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true positives classified as false negatives by bndeval

Hi Asher, I hope I have interpreted your question correctly, but I believe the problem is that the

7/4/23

K Noble, Len Trigg4

6/21/23

Sorry, you must be running a 64bit operating system

Yep, that'll work fine for you. We'll use the info you sent through to update the launcher

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Sorry, you must be running a 64bit operating system

Yep, that'll work fine for you. We'll use the info you sent through to update the launcher

6/21/23

Asher Bryant, Sean Irvine3

6/14/23

bndeval on liftedover vcf

That's fantastic! Thank you very much! On Wednesday, June 14, 2023 at 6:11:31 PM UTC-4 Sean

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bndeval on liftedover vcf

That's fantastic! Thank you very much! On Wednesday, June 14, 2023 at 6:11:31 PM UTC-4 Sean

6/14/23

Asher Bryant, Len Trigg2

6/12/23

Hi Asher, My guess is that your VCF's are invalid in some way (eg perhaps they're actually

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Hi Asher, My guess is that your VCF's are invalid in some way (eg perhaps they're actually

6/12/23

Brendan O'Fallon, Len Trigg3

6/9/23

VcfEval and overlapping vars

Indeed that did the trick! Thanks for the help. Replacing the 0 allele in the GT field with a '.

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VcfEval and overlapping vars

Indeed that did the trick! Thanks for the help. Replacing the 0 allele in the GT field with a '.

6/9/23

Stephane Plaisance

4/19/23

Re: [rtg-users] Digest for rtg-users@realtimegenomics.com - 2 updates in 1 topic

Hi Len, Yes I am back using your beautiful app. I found the command details after sending my

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Re: [rtg-users] Digest for rtg-users@realtimegenomics.com - 2 updates in 1 topic

Hi Len, Yes I am back using your beautiful app. I found the command details after sending my

4/19/23

Stéphane Plaisance, Len Trigg2

4/18/23

Editing dbSNP.vcf to use in vcfeval

Hi Stéphane, Hope all is well with you. You should be able to use the dbSNP VCF file directly without

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Editing dbSNP.vcf to use in vcfeval

Hi Stéphane, Hope all is well with you. You should be able to use the dbSNP VCF file directly without

4/18/23

Alexandra Vatsiou, Sean Irvine3

2/1/23

error in vcfeval with GT

Hi Alexandra, The VCF records in your example are invalid. In particular, what allele would be

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error in vcfeval with GT

Hi Alexandra, The VCF records in your example are invalid. In particular, what allele would be

2/1/23

Amjad Ali, Sean Irvine4

1/3/23

Baseline line file in Tumour:Normal samples

Hi, The vcfeval command only deals with small variants (ie, cases which are fully resolved into

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Baseline line file in Tumour:Normal samples

Hi, The vcfeval command only deals with small variants (ie, cases which are fully resolved into

1/3/23

L Mao, Sean Irvine3

12/24/22

Why this SNP was classified as FN by vcfeval?

I see. Thanks Sean! 在2022年12月20日星期二 UTC+10 19:36:22<Sean A. Irvine> 写道： Hi, The baseline file (

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Why this SNP was classified as FN by vcfeval?

I see. Thanks Sean! 在2022年12月20日星期二 UTC+10 19:36:22<Sean A. Irvine> 写道： Hi, The baseline file (

12/24/22

Brett Chapman, Len Trigg5

10/28/22

Error while indexing

Hi Brett, There is an example in the user manual. Basically you just give vcf2rocplot all of the

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Error while indexing

Hi Brett, There is an example in the user manual. Basically you just give vcf2rocplot all of the

10/28/22

Luis Willian Pacheco Arge, Len Trigg3

5/18/22

Problem in comparing two VCFs with eval module

Hi Len I re-ran all the previous steps to generate the final vcf files and the indexes, and then the

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Problem in comparing two VCFs with eval module

Hi Len I re-ran all the previous steps to generate the final vcf files and the indexes, and then the

5/18/22

Alexandra Vatsiou, Len Trigg3

3/30/22

tp-baseline vs tp-called

thanks On Monday, March 28, 2022 at 7:22:47 PM UTC+1 Len Trigg wrote: Equivalence is determined at

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tp-baseline vs tp-called

thanks On Monday, March 28, 2022 at 7:22:47 PM UTC+1 Len Trigg wrote: Equivalence is determined at

3/30/22

Arti Tandon, … Sean Irvine4

3/15/22

Error in using vcfeval with different with reference sequence

Hi Gil, We don't provide any options for swapping between the representations of chromosome names

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Error in using vcfeval with different with reference sequence

Hi Gil, We don't provide any options for swapping between the representations of chromosome names

3/15/22

Alexandra Vatsiou, Len Trigg2

2/28/22

vcfeval score and decompose

Hi Alexandra, 1) The score field comes from the calls file. 2) Yes it definitely can, as long as the

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vcfeval score and decompose

Hi Alexandra, 1) The score field comes from the calls file. 2) Yes it definitely can, as long as the

2/28/22

Alexandra Vatsiou, Len Trigg5

12/23/21

vcfeval fails with multi-allelic records

Hi Len, Apologies I forgot to add the command in the previous message. Here is the command, I was

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vcfeval fails with multi-allelic records

Hi Len, Apologies I forgot to add the command in the previous message. Here is the command, I was

12/23/21

Alexandra Vatsiou, Len Trigg2

10/27/21

vcfeval: baseline total value changes while --all-records is used

Hi Alexandra, Lack of GQ values should not be a problem. --all-records will include variants marked

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vcfeval: baseline total value changes while --all-records is used

Hi Alexandra, Lack of GQ values should not be a problem. --all-records will include variants marked

10/27/21

s m, Len Trigg2

10/11/21

How are the values in phasing.txt from vcfeval calculated?

Hi, Actually, that output is from some early code that we were working on to summarize phasing

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How are the values in phasing.txt from vcfeval calculated?

Hi, Actually, that output is from some early code that we were working on to summarize phasing

10/11/21

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