Linux based Galaxy analysis may help for this pipeline,

https://usegalaxy.org/u/aun1/p/ngs-analysis-service

https://toolshed.g2.bx.psu.edu/repository?repository_id=45e338238cab8812&changeset_revision=565c0e690238

SAMtools would Analyze mismatches in mapped variants to reference genome in SAM-BAM files & compute  likelihoods of SNP

ANNOVAR: Annotate SNPs with: statistics amino acid substitution effect predictions (SIFT, PholyPhen etc.) .

this tool also are very helpful

https://toolshed.g2.bx.psu.edu/repository?repository_id=f5c1f75e9fb33f8e

Thank you for answer. I actually know the programs you have presented, however they do not meet my expectations completely. I have just wrote a script in Python which does what I want.

I intend to develop it and it is possible that I will pipe it with SAM or BAM tools if needed.

It works fast enough. It processes 1MB nucleotide sequence per 1 s on my old dual core 2.1 GHz laptop.

hello doctor  this link very helpful 

https://toolshed.g2.bx.psu.edu/repository?repository_id=f5c1f75e9fb33f8e

Thanks for all comments. I set following steps:

Mapping with BWA to reference FASTA sequence | converting with Sambamba to bam | filtering, sorting and indexing with Bamtools -> visualizing with IVG on reference FASTA sequence,

finding of the target SNP presence in reference FASTA using my Python script with pulling out the surrounding sequence to obtain a motif with the SNP, 

finding the motif with IVG with the target SNP.