At the 98th and 99th codon of HLA-DQA1 gene in the reference genome, NA12878 should be ATCATG (reference) and AGTCTG respectively for the two chromomsomes. However, when I looked at the bams (downloaded from 1000g) in IGV, I noticed that both bwa and ssaha2 added an insertion and a deletion to the alignment:
A-TCATG
AGTC-TG
How should I fix this? Increase the gap penalty and re-run the alignment? Is there a way to manually edit the alignment inside bam?
A-TCATG
AGTC-TG
How should I fix this? Increase the gap penalty and re-run the alignment? Is there a way to manually edit the alignment inside bam?
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