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Old 01-09-2019, 09:55 PM   #1
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Location: India

Join Date: Mar 2017
Posts: 3
Default 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.

1. What is the criteria for calling the variant? 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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