Question: Varscan For "Split" Regions In Rnaseq Reads
1
gravatar for pulyakhina
5.7 years ago by
pulyakhina20
Netherlands
pulyakhina20 wrote:

Hi everyone,

I'm using Varscan to call SNPs in my mpileup files generated from RNAseq data. The signs "<" and ">" in mpileup correspond for regions that fall within pieces of a split RNA reads, and these regions are calculated in the total coverage that is in the fourth column of an mpileup file. When I look at the Varscan vcf file, I see that the total coverage per in vcf files includes those < and > (I'm not talking about low quality bases, which are nicely removed by Varscan and I can see that the coverage in vcf file is sometimes smaller than the coverage in mpileup file).

However, I think that these "split" regions should not be considered as real coverage. Does anyone know whether I can tune Varscan in such a way that it takes this into account and does not include the coverage in those "split" regions into the SNP coverage?

Thanks in advance,

Irina

vcf varscan rnaseq • 1.8k views
ADD COMMENTlink modified 5.6 years ago by dankoboldt140 • written 5.7 years ago by pulyakhina20

Why don't you want to use split reads? However, if you don't want to use them, you can just remove them from the alignment file.

ADD REPLYlink modified 12 weeks ago by RamRS21k • written 5.7 years ago by Fabio Marroni2.1k
1

I do want to use split reads. But when a read is split, the part in between the pieces of read that are actually mapped - this part is considered as a normal standard coverage in mpileup (marked with > or < sign) and I don't want this part to be considered as real coverage.

ADD REPLYlink modified 12 weeks ago by RamRS21k • written 5.7 years ago by pulyakhina20

Sorry, I didn't get it. I don't know how to help with this...

ADD REPLYlink modified 12 weeks ago by RamRS21k • written 5.7 years ago by Fabio Marroni2.1k
1
gravatar for dankoboldt
5.6 years ago by
dankoboldt140
dankoboldt140 wrote:

Thank you for posting this question. VarScan does not count > or < bases for the purposes of variant calling. I just looked at the code to be certain.

It will report the SAMtools-reported depth, but it ignores < and > characters in the pileup.

If you have an example that seems to disagree, please send it my way!

ADD COMMENTlink modified 12 weeks ago by RamRS21k • written 5.6 years ago by dankoboldt140
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