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Parse raw vcf in R from CollapsedVCF (VariantAnnotation library)

vcf bioconductor variantannotation written 5 weeks ago by ricardoguerreiro2121 • 20

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256

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locateVariants returns an empty result

indel R bioconductor variantannotation written 11 months ago by boris • 0

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1.3k

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ReadVCF not reading samples

R readvcf variantannotation written 3.8 years ago by Alexander Skates • 320 • updated 14 months ago by Biostar ♦♦ 20

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737

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Unable to read large Vcf file in R

R variantannotation vcf files written 21 months ago by sridevi • 0

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960

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How to make new VCF files myself?

vcf variant variantannotation written 2.6 years ago by Amirosein • 70 • updated 2.5 years ago by chen • 1.8k

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VariantAnnotation: error from readVcf command

R variantannotation written 3.8 years ago by pifferdavide • 90

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How can I filter a vcf file by DP and GQ using the R package VariantAnnotation?

vcf R bioconductor variantannotation written 4.0 years ago by r.jaffe • 10 • updated 4.0 years ago by Jeremy Leipzig ♦ 18k

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Recent Replies

A: how do I properly use edgeR::scaleOffset to combine two targeted RNA-seq panels? by Gordon Smyth • 620
The library sizes and norm factors correspond to columns rather than to rows, so your formation o...
A: how find the putative gen from cdna library? by lieven.sterck ♦ 4.2k
Given that you are looking in (assembled) transcripts sequences (so not genome, right?), I sugges...
C: How can I analyze this data in Deseq? by Kevin Blighe ♦ 39k
In which journals were they? They may have only used DESeq2 for, for example, size factor calcula...
C: combining z-scores into a single z-score value by Kevin Blighe ♦ 39k
Hey, oh, then why did you choose that test if you do not know how to interpret the result? You mu...
C: combining z-scores into a single z-score value by Star • 20
I don't know how to interpret the z-scores? I am assuming that I need to convert z-scores into p-...
C: DESeq2 result contrast by Devon Ryan ♦ 88k
I count more than one comparison in that sentence, rephrase it to include only one. You can contr...
C: How to add biological annotations using R by swbarnes2 ♦ 5.0k
What are the three most common sources of programming errors? Poor naming, and 1-off errors.
A: Interpreting HTSeq output file by lieven.sterck ♦ 4.2k
OK, clearly I was not paying attention :/ You are looking at the wrong file `counread.text` whic...
C: How to obtain SNP positions for specific mouse strain using VCF from Sanger Inst by Ankit • 60
Hi Pierre, Thanks for the reply. I tried the command but it is giving error: wget -q -O - "f...
C: 5', 3' SS and Intron retention read count using STAR out.tab by Malcolm.Cook • 1.0k
No: based on my reading of the paper and skimming the source code, it appears to me that SGSeq do...
C: How to calculate the tilt angle of a protein by natasha.sernova • 3.4k
I found a definition in their methods (long link in the bottom)! Revisiting Hydrophobic Mismatch...
C: how find the putative gen from cdna library? by genomax ♦ 64k
https://www.biostars.org/p/265158/ https://www.biostars.org/p/332064/ http://www.yandell-lab.org/...

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