Jonn Smith
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Recent activity by Jonn Smith Sort by recent activity-
Hi mehran fazel Yeah - the issue is your contig names. The HG38 contig names recognized by funcotator (and standardized in Homo_sapiens_assembly38.fasta are of the format: chr1 chr2 chr3 chr4 chr5...
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Official comment Hi mehran fazel, When you say chromosome annotation should be correct do you mean the `chr1` vs `1` naming? Just in case, can you check the `/mnt/rowData/refrence/GRCh38_latest_genomic.dict` file ...
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Hi Sam, The most recent release of GATK (4.5.0.0) has some fixes for funcotator that may have addressed this issue (in particular, the parsing for GTF/GFF3 files was updated). If you want, you...
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Please make a new issue in the GATK github with this information. https://github.com/broadinstitute/gatk
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Hi khushi ahuja, Oncotator is no longer supported. There is an hg19 data sources release somewhere for it, but I no longer know where it is hosted. Funcotator uses an older MAF spec, which ma...
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Official comment Rami Kheireddine Funcotator is designed for users to create their own datasources to annotate their own favorite species and genes / other markers. The pre-packaged datasources are only for human...
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Manuel Sérgio Sokolov Ravasqueira The chain file you linked does actually contain mappings for `Y` and `MT`. The article I wrote about the reference discrepancies can also be referenced: https://ga...
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Bhavneet Bhinder - The quickest thing I can suggest is to run Funcotator in `all transcripts` mode (`--transcript-selection-mode ALL`). This will give you every transcript annotation for all of yo...
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Official comment Hi Zhan, The default is 2 bases. It looks like this argument was never exposed to the user, so currently there is no way to configure it at runtime (this is a bug!). I'll add an issue in the GAT...
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Lim Chen We recommend that people create new posts in the general comments section for support questions. That said, I'm guessing your VCF is aligned to HG19 / B37. VCF files have header rows in t...