User: summerela

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summerela0
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Posts by summerela

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Comment: C: Add Custom Annotations to Multi-Sample VCF with VariantAnnotation() package
... Hi Valerie- I was trying to show two methods above of reading the same file in with readVcf and readVcfAsVRanges, sorry if I did make that very obvious!  You are absolutely right about the direct comparison of 2 VCF files. Here is the final code I came up with. Now if I can just get the info field ...
written 4.7 years ago by summerela0
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Answer: A: Metadata Missing from vcf when reading in with readVcfAsVRanges
... Hi Valerie- Thanks for your help. Using mcols() instead of info() for the VRanges object worked:  ##set reference humie_ref = "hg19" ######################### ## Read in Kaviar File ## ######################### ##add kaviar info fields kav_params = VRangesScanVcfParam(info= c("AF", "AC", "AN", ...
written 4.7 years ago by summerela0
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Metadata Missing from vcf when reading in with readVcfAsVRanges
... Hello-  It's me again. I am trying to read in the kaviar database (vcf format) using VariantAnnotation()'s readVcfAsVRanges. It reads in the file, but gives me an error and does not include any metadata information.  Here is what the VCF looks like:  ##fileformat=VCFv4.1 ##fileDate=20150211 ##so ...
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Comment: C: Add Custom Annotations to Multi-Sample VCF with VariantAnnotation() package
... I spoke too soon!  Using the method of comparing alt(vcf) and alt(ref)  directly on compressed vcf files returns an error when trying to subset the vcf file, I'm assuming because the vectors are of differing lengths. I tried the as below, and also tried first creating a subset of the vcf's by merg ...
written 4.7 years ago by summerela0
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Comment: C: Add Custom Annotations to Multi-Sample VCF with VariantAnnotation() package
... Valerie-  I can't thank you enough! I ended up using "any" instead of "all" to subset the vcf files so that I could keep rows where any of the alleles matched.  > ##read in test files > fl <- system.file("extdata", "ex2.vcf", package="VariantAnnotation") > vcf1 <- vcf2 <- readVc ...
written 4.7 years ago by summerela0
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Add Custom Annotations to Multi-Sample VCF with VariantAnnotation() package
... Hi- I'm trying to figure out the best method for adding custom annotations to multi-sample VCF files using the VariantAnnotation package. I have an already functionally-annotated multi-sample VCF file that I would like to match up with another VCF file containing different annotations (not multi-s ...

Latest awards to summerela

Popular Question 3.0 years ago, created a question with more than 1,000 views. For Add Custom Annotations to Multi-Sample VCF with VariantAnnotation() package
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Add Custom Annotations to Multi-Sample VCF with VariantAnnotation() package
Scholar 4.7 years ago, created an answer that has been accepted. For A: Metadata Missing from vcf when reading in with readVcfAsVRanges

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