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Question: vcfR for Whole Genome Data
0
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Dears all, Actually I have a generated vcf file by samtools pipeline and before doing the filtration of SNPs, I am going to check their quality, mapping and depth using vcfR. But at the first step when I want to read the vcf file I am facing with an error. Here is the command that I used:

T.vcf<- read.vcfR("species.vcf)

And here is the error I have:

Processed variant 136000Error in .read_body_gz(file, stats = stats, nrows = nrows, skip = skip, : long vectors not supported yet: memory.c:1668

I will be grateful if anybody can help me with this error.

Regards, Omid

1
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Use the right tool for the job, R is not great for whole genome data. Maybe use bcftools for filtering, then use R for further analysis.

ADD COMMENTlink 12 months ago zx8754 7.5k
Entering edit mode
0

Thanks for the answer, So you mean I can use the vcfR package for only the vcf files which are small in size? because I have used this package for a vcf file generated for GBS data but for the WGS data I have this problem.

ADD REPLYlink 12 months ago
jaafari.omid
• 40
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No, he means to do everything outside of R. Take a look at the functions available in BCFtools. By the way, bcftools query allows you to easily output data in tabular format, which you could then further analyse in R.

ADD REPLYlink 12 months ago
Kevin Blighe
43k

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