SNP calling using samtools

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5.3 years ago

ankit hinsu ▴ 10

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!!

SNP samtools bcftools mpileup rnaseq • 1.6k views

ADD COMMENT • link updated 5.2 years ago by Biostar 20 • written 5.3 years ago by ankit hinsu ▴ 10

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What is the criteria for calling the variant

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

ADD REPLY • link 5.3 years ago by Pierre Lindenbaum 161k

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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 REPLY • link 5.3 years ago by Pierre Lindenbaum 161k

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

ADD REPLY • link 5.3 years ago by ankit hinsu ▴ 10

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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 REPLY • link 5.3 years ago by h.mon 35k

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