Question: SNP calling using samtools
3 months ago by
ankit hinsu • 10
ankit hinsu • 10 wrote:
I have RNA-seq paired-end data from Illumina and I am using BWA-mem for mapping and samtools for SNP calling. I wanted to understand and get your opinion regarding following.
- [B]What is the criteria for calling the variant[/B]? Specifically, at a particular position, how many reads should contain variation for it to be called as a variant. I want to call variant at a position if it supported by more than 20% of reads at that position.
What parameter can I use to achieve this.
Any help is appreciated!!
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