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Erik;
I was working on validating the latest head today and ran into issues like:
```
Exception: Unable to read reference sequence base past end of current cached sequence.
```
I know you checked in…
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Once the first stable release is reached.
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There are some variants and call info fields which are repeated in VCF. (e.g. any tag that is repeated per-allele - AC, AF, HQ, EC etc)
How should these fields be represented as GAKeyValue - which ha…
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**Proposed topic for ASHG**
How to support Variant calling with the API?
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A new graph version of the GA4GH API was added via PR 238 in the GA4GH/schema repository:
https://github.com/ga4gh/schemas/pull/238
It supports both classic and graph-supported server modes, with some…
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We currently have 2 APIs that are tangentially related to our main v0.5 - [beacon](https://github.com/ga4gh/schemas/blob/master/src/main/resources/avro/beacon.avdl) and [matchmaker](http://cassiedoll.…
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Hi Erik,
We are having some issues using Freebayes, with respect to the BAI Index Files in our pipeline.
This is the error that is present:
```
ERROR(freebayes): Opened BAM reader without index fil…
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Consider a researcher who writes a script against the GA4GH APIs, accesses data and publishes the results. The current APIs do not guarantee that subsequent researchers will get the same result when r…
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It would be very useful (e.g in kmer based analyses) if the `/reads/search` method provided a mechanism to find all reads that contain a given substring. In general this may be quite hard to do, but p…
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I'm trying to use the freebayes-parallel script to parallelize calling of exomes, where I'm also giving it a bed file of targets. But, when given both the targets and a region, freebayes seems to be …