Variant Calling with SAMtools
You’ve sequenced it, and now you have aligned it. Next check your alignment for variants with the new variant calling feature. Whether you have aligned your reads with one of our reference-guided aligners or you have sourced your aligned SAM/BAM files elsewhere, you can still check for variants using Variant Calling with SAMtools.
This analysis can be used after SNP-tolerant alignment, methylation-tolerant alignment, or the new RNA A-to-I editing tolerant mode in GSNAP. Then load the resultant VCF file and SAM files into your favorite browser, if you don’t have one try out Tablet – it’s part of our DNA-Seq Tools distribution. Provide Tablet with a GTF file for annotation and you will also be able to see variants within features.
For more information on Variant Calling with SAMtools, please check out our Advanced Next-Gen Sequence Alignment Tutorial.