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vcftools and SnpSift give different values for Ts/Tv ratio

vcf transversion variant transition snp written 4.3 years ago by ethan.kaufman • 360

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answer

1.5k

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PAR-clip T to C mutations becoming T to G in minus strand?

par-clip transversion mapping igv written 4.6 years ago by t.candelli • 60 • updated 4.6 years ago by Istvan Albert ♦♦ 80k

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210

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Reference TiTv ratio for mouse WGS?

mouse transversion transition snp titv written 4 months ago by serpalma.v • 20 • updated 10 weeks ago by Biostar ♦♦ 20

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Recent Replies

C: How to remove duplicate sites and inconsistent sites from a VCF? by rodd • 20
I also imputed my data using the Michigan Imputation Server (MIS), using the 1000 Genomes Phase 1...
C: Extracting uniquely mapped reads from bams by gokberk • 20
Thanks for your responses Nitin and ATpoint. I've already seen the thread ATpoint mentioned, howe...
C: Hisat2 aligner problem by genomax ♦ 67k
This is kind of dependent on hardware you have. As long as you are seeing CPU's in use (and the o...
C: Hisat2 aligner problem by ta_awwad • 210
it was running overnight for 50 million reads only
C: Hisat2 aligner problem by ta_awwad • 210
i was patient overnight :)
C: Extracting uniquely mapped reads from bams by ATpoint ♦ 16k
Also see https://www.biostars.org/p/295354/ and please use google and the search function. This h...
C: Repeated product tag in a genbank file by jrj.healey ♦ 12k
Duplicated features does happen from time to time, and they can often be ignored safely depending...
C: Repeated product tag in a genbank file by genomax ♦ 67k
This may be a glitch from `Gnomon` (NCBI's eukaryotic gene prediction tool). Let NCBI know by ema...
C: BBSplit xenograft Human-Mouse- RawCount by genomax ♦ 67k
Have you examined your aligned files in IGV? Go to genes you know should be there and see what th...
C: Extracting uniquely mapped reads from bams by Nitin Narwade • 390
I think [this biostars thread][1] might be helpful in your case. [1]: https://www.biostars.or...
C: BBSplit xenograft Human-Mouse- RawCount by giovannaventola3es9 • 20
yes, it is so!!! However, I used -s 2 and I obtained a low level count. I don't know if there is ...
C: Orthology and Pylogenetic Analysis by jrj.healey ♦ 12k
Yes, this is a pretty normal thing to do. Before we advise you though, we need to know more abou...

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