VariantAnnotation

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API to change output suffix to .gz

7

The majority of VCF handling bioinformatics libraries use a `.vcf.gz` suffix, even for block gziped output. `writeVcf()` with `index=TRUE` does not support this and forceably sets the suffix to `.bgz`....

d-cameron

Populate INFO column with VariantAnnotation::writeVcf

4

Hi , I'm the creator of the MungeSumstats Bioconductor package in which we use VariantAnnotation::writeVcf as an output options for the formatted sumstats. I want to align the formatting of...

Al-Murphy

merging VCF objects

9

It would be nice to have an efficient utility to merge two VCF objects that have differing (but often overlapping) sets of variants and samples. I guess the assay matrices...

lawremi

locateVariants returns genes from both Forward and Reverse strands in PRECEDEID and FOLLOWID

3

Hello, I'm looking at an intergenic variant (in the bovine genome) and want to figure the genes relative to which it is downstream or upstream, i.e. relative to the gene's...

amizeranschi

As the title indicates, I have to add "which=rowRanges()" to make the `readVcfStack` work when using `param`. `readVcf` works as expected. Issue only exist in Bioc devel. Coding in bioc...

Liubuntu

Can geno() obtain the reference depth and alternate allele separately?

1

lihe-s

Create protein sequences including variants from a VCF file

3

Dear BiocTeam, I am investigating the proteome of human cancer samples and want to insert their genetic variations into the reference proteome fasta sequences to increase the sensitivity of my...

baderd

predictcoding - multiple mutations at a codon are never evaluated additively

1

I have HIV sequence data, where for three consecutive positions I have SNPS. These three all code for SNPS in the same codon. predictcoding() returns the independently evaluated REFAA and...

ojcharles

Hello VariantAnnotation team, I am using the predictCoding function to annotate the coding consequence of SNPs in my VCF file using a custom GTF file. Here is what I ran:...

onebeingmay

Minimal example: ```r library(VariantAnnotation) fl

DarioS