Bashir Sadjad

Resolve dependency issues in setup.py.

3

Currently we get some dependency conflicts after installing [setup.py](https://github.com/googlegenomics/gcp-variant-transforms/blob/master/setup.py) and that is because `pip` cannot resolve version dependencies properly. IOW, instead of picking the intersection of version specifiers between different...

Write Avro files.

2

Beside writing into BigQuery, we need to also support serializing variant records into some binary format. This is useful when the variants are needed to be used in contexts other...

When parsing annotation fields, it is probably safe to assume that `ALLELE_NUM` tag refers to one of the ALTs even without the user telling us explicitly. So the proposal is...

Add counters for mismatches resolved by robustness features.

1

When we use robustness features like [--allow_incompatible_records](https://github.com/googlegenomics/gcp-variant-transforms/blob/fb1ff77ed98c15c80966b95f6e913087618e2fdd/gcp_variant_transforms/options/variant_transform_options.py#L60), it is very useful if we track the number of cases that are resolved by enabling these features (and also to group by...

Better communicate reference sequence mismatch, when running variant annotation.

2

Currently we have [--check_ref](http://ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_check_ref) enabled when running VEP. This generates a list of reference mismatches if the VEP cache used is for a different reference sequence than the one used...

Currently, if a VEP run fails, we proceed and possibly fail later in the Dataflow pipeline (e.g., because of missing input files) without clearly showing the root cause. Instead, we...

When the VCF is for comparing a somatic vs a germline cell, the format of the allele part of annotation fields is different. We should add an option for parsing...

Currently, we have implemented running of VEP (Variant Effect Predictor) as a preprocessor step in Variant Transforms by directly calling the Pipelines API directly. The main reasons we decided against...

Given that now we have enough large/medium integration tests (see Issue #99), it is important to export performance numbers for each large test and monitor the changes. This will enable...

ID fields of converted Avro records are not expected to be fully qualified URLs.

1

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