SNP calling using samtools
Hi all,
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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ankit hinsu •
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ankit hinsu •
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see "Mathematical Notes on SAMtools Algorithms" http://lh3lh3.users.sourceforge.net/download/samtools.pdf ...
Hello ankit4035hinsu!
It appears that your post has been cross-posted to another site: http://seqanswers.com/forums/showthread.php?t=87098
This is typically not recommended as it runs the risk of annoying people in both communities.
Thanks for the algorithms. Also, I will refrain from cross-posting on other site.
Unless you are mapping to a bacterial genome, BWA is not the best mapper for this task, as it is not splice-aware. You should use STAR or HISAT2.