Exome Seq Data analysis - chromosome start and end positions

Question

[prathyushakonda]

Hello,

I am an immunology student learning bioinformatics. I was searching to find the right answer for the problem I have but haven't found any concrete explanation.

I have an exome seq data file downloaded from a public database. The excel file contains details regarding ProbeID, gene name, gene id, chromosome, start, end, snptype for the cell line of my interest. I wanna perform variant calling on this data and obtain the mutated sequences. I would like to know how to start aligning or retrieving the sequence.

Thank you!!

[vakul.mohanty]

Could you clarify what data you have downloaded? You don't seem to have the raw exomeseq to make variant calls(fastq or BAM). If you have raw data you can use various tools like Varscan (http://varscan.sourceforge.net/), Mutech (https://www.broadinstitute.org/cancer/cga/mutect) etc to identify mutations.

Also if you have information like probeID its probably processed data from SNP arrays, exomeseq wouldn't have probe IDs.

[prathyushakonda]

That makes sense. I think it's snp array. I was confused because the website and the file name said exome seq data.

Thank you, Vakul Monhanty!

[vakul.mohanty]

No biggy, all the best with your analysis.