SNP calling using samtools

Question

[ankit hinsu]

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.

1. [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!!

[Pierre Lindenbaum]

What is the criteria for calling the variant

see "Mathematical Notes on SAMtools Algorithms" http://lh3lh3.users.sourceforge.net/download/samtools.pdf ...

[Pierre Lindenbaum]

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.

[ankit hinsu]

Thanks for the algorithms. Also, I will refrain from cross-posting on other site.

[h.mon]

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.