how to identify SNPs and indels between two samples

[pandafengye]

I am new to NGS data analysis. I got two individual samples, each sequenced and mapped against the same reference genome.
Now I want to identify SNPs and short indels between the two samples. What software/pipelines should I use?

[adaptivegenome]

Look up "GATK" on your favorite search engine.

[vishnuamaram]

Hi pandafengye,

you can also samtools mpileup
&/ or followed by VarScan.

[Knaus]

after you have the variant call file (VCF) upload it to gene-talk.de and filter for snps, indels, etc...