Hi, We are doing whole exome data analysis using GATK best practices guidelines. There are few genes which has pseudogenes, the mapping quality becomes zero. Such as SMN1 and SMN2, GBA and GBAP1 etc. We are getting white colored reads with mapping quality zero. That is probably due to the reads mapped in multiple regions. There are some known mutations in these pseudogenes such as C to T transition in exon 7 of SMN2, which should appear as heterozygous in the reads which cover the gene. The problem is we are finding normal homozygous in both gene and pseudogene in IGV.
If we select only the uniquely mapped reads then we will miss these mutations present in the pseudogene. Also specifically for SMN genes, both SMN1 and SMN2 genes are showing as same co-ordinates in IGV whereas both has different co-ordinates. For SMN1: chr5:70220768-70249769 and for SMN2: chr5:69345350-69374349. We are using hg19 reference genome. If anyone can explain this incidents and may suggest something it would be very much helpful.
Thanks & regards, Aneek
