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Hello,
I am trying to build a database for trees species (Western Redcedar). I have a draft genome and some annotations in GFF3 format. When I try to build the database I get the following error:
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Hi,
Our team is using MSMS to study heart diseases and are getting access to RNA-Seq data. Your software looks to potentially be very useful.I have installed Docker Desktop and been trying to run y…
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I'm interested in checking that tests in the */workflows directories are working and writing some new ones for untested workflows. If I am writing a test for one I'll write it down here as an effort …
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When running SnpSift, I ran into this error:
“Exception in thread “main” java.lang.RuntimeException: Cannot parse EffectType ‘transcript’
I pinned down the error to the second term of an annotat…
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Hello ! First time working with genomic data and this has made my life extremely easy ! just wondering if it would be possible to also add the DP field in the bcftools mpileup so the vcf file can be p…
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Thanks for the great commenting throughout! Random typo: "no" should be "not" here, https://github.com/pcingola/SnpEff/blob/master/src/main/java/org/snpeff/interval/Downstream.java#L36
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I am trying to annotate the snp chr5:138609638 C>G (gene: MATR3, transcript: NM_199189.2, strand +).
I use snpEff 4.2 on hg19 database but the issue also arises on GRCh37.75.
The command line:
```
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I'm having a problem where some of the records in my VCF files have a single N in the ALT field. SnpEff/SnpSift keeps changing these to A,C,G,Ts. Is there any way to turn this feature off in the futur…
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I use annotate a vcf which is custom database. I found for insert mutation, I cann't get right annotation.
java -jar snpEff.jar -dataDir /data/bioxFlow/annox/snpEff/data/ -geneId -canon -v GRCh37.p13…
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Dear @pcingola ,
We use SnpEff to annotate structural variant VCF files.
For large putative structural variants of a few million bases the VCF ANN field becomes very large.
This breaks downst…