Ben Weisburd

I think that would help.. what I'm trying to get to is a table where each row is a repeat locus, and which I could merge across samples to then...

Yes. I use 2 kinds of tables in my analyses - a locus table: repeat | motifs | sampleA short allele | sampleA long allele | sampleB short allele |...

I am able to build from my fork both on MacOSX v14.4 and Linux @ https://github.com/bw2/reviewer using these commands https://github.com/broadinstitute/str-analysis/blob/main/docker/Dockerfile#L133-L143

The `--manifest` arg should be a text file. You should try running ``` echo depth_calling/tests/test_data/NA12885.bam > manifest.txt python3 smn_caller.py --manifest manifest.txt --genome 19 --prefix NA12885 --outDir ./ --threads 2 ```

"invalid contig" may indicate a mismatch between the reference genome and read data file. If you post the full python stack trace along with the error message, it may help...

I'm not 100% sure, but this error may be due to zero coverage at SMN positions where the tool is expecting reads. I would open the input bam file in...

Yes. SMNCopyNumberCaller only works for WGS data because it looks at reads within both exonic and intronic regions of SMN. For targeted sequencing data, you can use https://github.com/broadinstitute/sma_finder (though it...

I see, that makes sense. Thanks.

You may find this script useful https://github.com/broadinstitute/SpliceAI-lookup/blob/master/annotations/convert_gtf_to_SpliceAI_annotation_input_format.py It's used for updating the annotations that underly https://spliceailookup.broadinstitute.org/ On Tue, Jan 2, 2024, 7:10 AM dudududu12138 ***@***.***> wrote: > Hello, > I...

Until this is merged into the official repo, I've merged it into my fork @ https://github.com/bw2/SpliceAI so it can be used @ https://spliceailookup.broadinstitute.org/