Why Samtools cannot call all the SNPs from bam files?

Question

[aggies.collins]

Dear all,

My data is RNAseq with single end reads. I used the Bowtie to generate the Bam file. And I want to call SNP using Samtools. I want to find the sites under RNA editing (from C-T or G-A). I hypothesize them as the SNP sites. I view the bam file by IGV, and lots of regions have these SNP variations. So I use the samtools and bcftools to call SNP. But it only produce very few sites as SNP.

Why samtools can not find all SNP sites by my data? Anyone can give me some suggestions?

Best

ZQ

[swbarnes2]

I don't think anyone can help with so little information. If you posted an IGV shot of a SNP that samtools is refusing to call, that would help.

[aggies.collins]

I add the shots here. Please have a look.

Thanks
ZQ

[Ashutosh Pandey]

I wanted to write a reply but found this post. See this post: IGV and Variant Call . In short not all the nucleotide differences that you see in IGV will be qualified to be called as variants. There may be some other reason in your case but as swbarnes2 said that we cant say anything until we see some example.

[aggies.collins]

I know, but the variation in my data is really good, I paste a shot pictures from IGV. you can see at this SNP site, the depth is over 1,000. But it still not shows. I have many sites like this with high depth but not report from samtools.

[aggies.collins]

Thanks for your reminding:

Here is the IGV shot and partial vcf files:

This is the results from chr1:

[aggies.collins]