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Command executed:
bcftools annotate --header-lines /Data/data/raja/cfdna/nextflow1/bin/syn3_header.txt LCR_FILTERED > FILTERED_hd.vcf
**java -jar -Xmx4g /Data/data/raja/cfdna/nextflow1/bin/snp…
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Support ANN fields name .
See :
http://snpeff.sourceforge.net/VCFannotationformat_v1.0.pdf
dridk updated
7 years ago
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### Description of feature
When using
```
nextflow run nf-core/sarek -r 3.1.1 -profile cfc \
--input 'sampleSheet_sarek.csv' \
--genome null \
--save_reference \
--fasta './Synechocystis_sp_…
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Take as input an unannotated VCF file, and output a VCF file with annotations.
@vlaufer, @erinkwagner, @HuaLing1, if you have time, please comment on which information that @cjav can expect in your o…
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Dear @hemstrow
I was wondering if it would be easy to write a function to calculate dN/dS ration using snpEff annotated VCF file. Currently, there is no functional tool or package available to do …
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When running the two snakemake wrappers `Varscan` -> `SnpEff` in succession there is an error thrown https://github.com/pcingola/SnpEff/issues/267#issuecomment-736928876
This does not happen when …
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Java programs should set tmp dir and max memory:
```nextflow
script:
sample_name = vcf.baseName
mem = task.memory ? task.memory.toGiga() : task.cpus * 6
// Also optionally check…
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Hello,
Is GREEN-VARAN compatible with VCFs annotated by VEP?
Thanks,
Madeline
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https://github.com/NBISweden/GenErode/blob/main/workflow/rules/9_merge_vcfs.smk#L266C23-L266C42
This command does not remove sites that are coded as heterozygous sites but are fixed derived sites (…
verku updated
2 weeks ago
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Hi @ashutoshkpandey Ashutosh,
It will be great if you can update this to accept latest ANN format of Snpeff
thanks