Question: SNP calling using samtools
0
gravatar for ankit hinsu
19 months ago by
ankit hinsu10
ankit hinsu10 wrote:

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!!

ADD COMMENTlink modified 18 months ago by Biostar ♦♦ 20 • written 19 months ago by ankit hinsu10

What is the criteria for calling the variant

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

ADD REPLYlink written 19 months ago by Pierre Lindenbaum129k

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.

ADD REPLYlink written 19 months ago by Pierre Lindenbaum129k

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

ADD REPLYlink modified 19 months ago • written 19 months ago by ankit hinsu10

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.

ADD REPLYlink written 19 months ago by h.mon30k
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