Question: Comparative Snp Analysis
1
gravatar for GPR
7.0 years ago by
GPR320
Mexico
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

QUESTION 2:

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 • 1.8k views
ADD COMMENTlink modified 5.9 years ago by Biostar ♦♦ 20 • written 7.0 years ago by GPR320
1
gravatar for zx8754
7.0 years ago by
zx87548.8k
London
zx87548.8k wrote:

Regarding Question 1 see Genotype fields at http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-40

ADD COMMENTlink written 7.0 years ago by zx87548.8k

Thanks so much!

ADD REPLYlink written 7.0 years ago by GPR320
0
gravatar for dankoboldt
7.0 years ago by
dankoboldt140
dankoboldt140 wrote:

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

ADD COMMENTlink written 7.0 years ago by dankoboldt140
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