Urgent help needed

[unsolvedquestions]

Hi everyone. I am sorry for asking a question that may sound very trivial to many of you but I am new to this field and do not have a bioinformatics background. Actually WES was done for 4 tumor samples which showed a mapping rate of 70-85% after alignment with BWA. Now I am reading everywhere that Mapping rate must be >90% but I am getting a low mapping rate. I want to know what can be the possible reasons for getting such low mapping rate and can we proceed with variant calling with such low mapping rate. Will the variant calling data be acceptable?

Thank you

[GenoMax]

While your mapping rate is lower (you could take a selection of reads that don't map and blast them at NCBI to figure out what they are) you should be able to proceed with further analysis. Assuming you have enough coverage to do SNP calling (>15-20x).

[gringer]

I'd recommend doing an analysis on the unmapped reads to make sure that they are not hitting something other than your intended target. With a tumour sample it's unlikely to be a contamination issue, but just in case, you could feed the unmapped reads through Centrifuge or OneCodex just to be sure of that.