I am using an older version of samtools (0.1.7a) for my project. Do I have any chance of missing out on data, SNPs or Indels, with the older version?

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Michael B Black

The variant calling tools are actually the bcftools bundled with samtools. Since it's free software, why not just download 0.1.18, compile and use that so you have the most recent set of both samtools and bcftools?

At the least you can download the 0.1.18 tar archive and there is a changelog in there that lists any changes to samtools or bcftools.

BTW, I highly doubt that the minor changes and bug fixes from 0.1.17 to 0.1.18 would actually make any difference in your results, but it's always best to keep up with the latest bug-patched and improved version of any program, so I'd suggest just updating your samtools installation.

Sébastien Küry

Hi Shalini, You probably have already chaged of variant calling tool, but from my own experience, I can assess that you may miss variant with Samtools. More especially indels. Yet, I think it's also the case with GATK.