seqr individual id

[sophienguyen01]

Hi,
I'm using local install via docker, and when I click Edit Datasets, it asks me to load ID Mapping File Path. I have no idea what this is. Where do I get the seqr individual ids?

THank you

[hanars]

The sample IDs in that error message are in your loaded data but not in your seqr project. Your options are:

1. You do not want to load data for these samples. In that case, you should select the "Ignore extra samples" checkbox
2. You want to load data for them with these sample IDs. In that case, you need to create the families and individuals before loading
3. You want to load data for them, but the sample IDs in the data do not match the Individual IDs for the individuals in the project. In that case, you upload the mapping file mapping these sample IDs to their corresponding seqr individual IDs

[sophienguyen01]

HI,

This is my situation: I loaded the data using instructions on this link:

Got this command finished successfully: docker-compose exec pipeline-runner load_data.sh $BUILD_VERSION $SAMPLE_TYPE $INDEX_NAME $INPUT_FILE_PATH.
Then I go to Seqr website, and I don't see any project listed. I did see my index in Data management/Elasticsearch Status though. So I created new project => 'Edit Datasets' and it is where I encountered problems.

With option1, I tried and this is the error:

For option2 and 3, how do I create the data that you mentioned? Could you guide my to an example? I am trying to find an example on seqr github but could not find anything.
Also, I have only 1 sample in my input vcf and how does it work?

[hanars]

No you need to do it now before using the "Edit Datasets" functionality

[sophienguyen01]

Should I go to 'Bulk Edit Familes' or 'Bulk Edit Individuals' in 'Edit Families & Individuals'.

I only have one sample in my vcf, let say the sample column in vcf is NA12878.
What I should fill in the tsv to submit for sample NA12878?
Family ID Individual ID Paternal ID Maternal ID Sex Affected Status Notes

THank you

[hanars]

Bulk Edit Individuals. Download the demo file that is available in the UI and fill out the table accordingly

[sophienguyen01]

I only have one sample in my vcf, let say the sample column in vcf is NA12878.

Here is the header in the demo file:
Family ID Display Name Description Phenotype Description MONDO ID

Should the 'FamilyID' be NA12878?

[hanars]

This is entirely up to you, this is not a question the seqr team can help with. You should be naming things in whatever way will be helpful to your group and your analysis. The upload form has a very detailed user interface that explains what each column does, what it means, and if it is required or optional. You should read that description and create the file in a way that is accurate and useful to your seqr project