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Hello - I am using SnpEff to annotate SARS-CoV-2 data (NC_045512). As you might know, SARS-CoV-2 has several large ORFs, which are processed into discrete peptides. These features are annotated in t…
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I have two issues to ask about which are not completely independent.
I am currently using the new version of snpEff (4.xx) which has new annotations. I have been putting them in manually but I am hav…
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Hello,
I am very interested on testing your workflow with our cancer samples.
I am trying to execute the workflow from the GUI to generate the protein sequence database + variants using SRA acc…
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Hi Torsten,
I am getting the following error when I run snippy 3.0:
### snpEff build -c reference/snpeff.config -dataDir . -gff3 ref
java.lang.StackOverflowError
at java.lang.Character.toLowerCa…
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The documentation (https://pcingola.github.io/SnpEff/se_buildingdb/) refers to `snpEffect.config` but I believe this should be `snpEff.config`.
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Dear there,
I tried to install SalmonTE. But, I failed to make it run on test data and did't figure out why did it happen.
Really appreciate for any help!
Best,
Xiaofei
```
$ Salmon…
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I have a good quality GG/TC MNP:
```
$ freebayes -f /data/reference/ucsc/hg19/hg19.fa -r chr22:42526560..42526563 -F 0.3 reads.bam 2> /dev/null| cut -f1-6 | grep -v "##"
chr22 42526561 . GG …
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Hi!
I am having some issues with the Delly and Chromotripsis detection.
I have done al the steps in the interactive mode and everything seems ok until I get to the $name.breakpoints.filtered.tab w…
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See https://github.com/nf-core/awsmegatests/issues/15
We will soon start having the results from the full-size test datasets stored on s3. It would be great to make these visible through the nf-cor…
ewels updated
3 years ago
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Hi,
I am maybe twisting use of bcftools as I served it with VCF file output by GATK-4.1.0.9 Mutect2, containing normal and a tumor sample pair. I guess bcftools is parsing INFO fields for both samp…