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It seems that indels are not getting parsed correctly, resulting in the AF and dbSNP lookups to fail.
For example, the VCF file contains:
`chr11 61165731 . C CA`
This results i…
buske updated
9 years ago
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not an issue, just a comment that SSAKE can now be brew installed
brew install ssake
*If you were to work with shotgun sequence data (WGS, RNA-Seq, exon capture) instead of amplicon, you could swap…
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The filtered allele is missing a deletion in exon 2. Most likely this bug affects other alleles with expression changes (insertions and deletions in coding regions).
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Field testing with mutlitple data sources validated HLA-A; however, -B and -C alleles aren't being produced even though filtered consensus sequences are there (possible that filtering is incorrect).
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So far, I've only looked at the HLA coverage for the 22 May 2014 run, but that run consistently has good coverage in two sections of the HLA-B region and no coverage in the rest of the region.
This me…
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Priority is after 6.3 launch. Motivation is to avoid drops in counts at region boundaries. This will also resolve the HLA problem with frame shifts due to intron. The two reading frames can be treated…
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Looks like another failed alignment:
```
2014-08-26 20:52:25.900231 - [INFO] Launching ' ./csf2counts.py /data/miseq/140522_M01841_0063_000000000-A64FB/46824A-3515-HLA-B-E99601CLIMX-PR-RT_S23.aligned…
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With same contents, but including pipeline version and a field for pass/fail.