You can use stacks for calling variants

see http://catchenlab.life.illinois.edu/stacks/ and https://github.com/enormandeau/stacks_workflow

You can use BWA + GATK pipeline for somatic and germline mutations.

For somatic mutation, you can use emsembl of following tools including MuTect (from Broad), Strelka, Varscan, Virmid, etc. For germline mutations, you can use haplotype caller from Broad which are most popular tools in this field of study.

BWA and GTK is nowadays a golden standard. Bowtie is also very used. I like varscan also for the easy of use....

The easiest you could do is employ the BCBio-Pipeline. It already comes with many tools preinstalled (it doesn't come with GATK though, since there are some licensing issues, but you can add the GATK yourself). https://bcbio-nextgen.readthedocs.io/en/latest/#

This pipeline is maintained, updated and can detect germline variants, somatic variants and a lot more (also RNA-Seq and ChIP-Seq)

I have recently come across a paper in PNAS using the programs PEMapper and PECaller which it claims perform better than BWA+GATK for cluster enviroments such as the ones found in many academic institutes: http://www.pnas.org/content/114/10/E1923.abstract

Also if you want something easy to use, you may try a software I developed and recently published called Altools.

There is no "perfect" pipeline for variant calling. Most, if not all, variant callers have systemic errors due to unpredictable behavior of BWA aligners when repeated sequences are encountered. For this reason, it is advisable to mask repeats PRIOR to alignment. K-mer based approaches do not handle variant dense regions very well.

@Mark Farman

If you are performing such analysis what all tools would you choose?

@Salvatore Camiolo

Thank you. I will go through the tool

@Rohan Chaubal 

I have set of genes with their chromosome location and known mutation. These genes are frequently mutated in the disease.

When a tumor sample is analysed, I need to confirm the mutation in the set of genes with their location. Which pipeline do you recommend for the variant analysis 

Altools can manage annotation gff3 file. If your gene coordinates are in this format (generally quite easy to create) you can use Altools to align the reads from the tumor cell sequencing and ask the program to map the found polymorphisms in the genic regions. The software will give also information on the type of mutation, e.g. synonymous mutation, amino acid variation, premature stop codon and so on. On the other hand if you have RNAseq data you will need some specific software that allow gapped alignement on reference such as Tophat.