Fungal genome SNP calling

Question

[nilamborah]

Hi everyone I would like to know if there exist any standard pipeline to align Illumina HiSeq data against two parental genome and to do QC + SNP calling for fungal genome? I am a biologist and have almost no knowledge in bioinformatics.

Answer 1

[Brice Sarver]

It doesn't matter that they're fungal genomes - you can use any standard variant calling approach (like the GATK's best practices) after you've mapped (using BWA or another mapper; this is described in brief in the link).

If you have F1s and you want to map to two parents as part of your analysis, you might consider using MODtools and Suspenders. Suspenders takes BAMs of reads mapped to two different reference genomes and will return reads that map to one parent preferentially.

Answer 2

[nilamborah]

Thank you. The idea is to take the F1 offspring and map against the parents and find out unique regions mapping to a particular parent.