Question: Comparative Snp Analysis
gravatar for GPR
7.9 years ago by
GPR320 wrote:

Hello, I am trying to compare the degree of A-to-G editing in a near-to-isogenic pair of cell lines. I have two biological replicates and have mapped with Bowtie and BWA, followed by a samtools mpileup | VarScan analysis. After this, I have used bedtools intersect to extract variants not annotated in dbSNP, but are in Alu repeats. Here is where I have some doubts, mainly two questions: QUESTION 1: In the vcf file (VarScan output),

#CHROM  POS     ID      REF     ALT     QUAL    FILTER    INFO    FORMAT  Sample1    Sample2
   chrM    73      .           G       A       PASS     DP=238  GT:GQ:DP           1/1:71:121  1/1:69:117

What exactly is the meaning of

FORMAT   Sample1    Sample2
GT:GQ:DP 1/1:71:121  1/1:69:117


I have higher number of editing sites "called" in sample 1 than in sample 2 in the 1st biological replicate (about 16% difference). However this difference is reversed in the 2nd biological replicate. What is the proper way of comparing the degree of RNA editing in two different samples? Is there a quantitative procedure? I have naively compared them with bedtools intersect, using or omitting option -v. Is this the correct way to go about it?

Many thanks. G.

bedtools varscan intersect • 1.9k views
ADD COMMENTlink modified 6.8 years ago by Biostar ♦♦ 20 • written 7.9 years ago by GPR320
gravatar for zx8754
7.9 years ago by
zx87549.7k wrote:

Regarding Question 1 see Genotype fields at

ADD COMMENTlink written 7.9 years ago by zx87549.7k

Thanks so much!

ADD REPLYlink written 7.9 years ago by GPR320
gravatar for dankoboldt
7.8 years ago by
dankoboldt140 wrote:

Thanks for answering, zx8754! And GPR, if you have any VarScan-related questions, please let me know.

ADD COMMENTlink written 7.8 years ago by dankoboldt140
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