I need your helps.
I have NGS data obtained from a lung cancer patient, and the driver mutation is a complex mutation where insertion and deletion are combined.
The inserted bases are
CCCCT and the deleted ones are
Below is the one of the reads that are harbouring the complex mutation.
The CIGAR string of the read alined by BWA is
BWA did not recongize the inserted bases, aligning them as mismatched bases.
I need the alignment results with both insertion and deletion.
How can I do this?
Below is the ideal alignment results that I hope.
ref : TATGTAGTCCATAAAACCCATGAGTTCTGGGCACTGGGTCAAAGTCTCCTGGGGCCCATGATAGCCGTCTTTAACAAGC-----TCTTTCTTTCTCTCTGTTTTAAGATCTGGGCAGTGAATTAGTTCGCTACGATGCAAGAGTACACACTCCTCATTTGGATAGGCTTGT query : TATGTAGTCCATAAAACCCATGAGTTCTGGGCACTGGGTCAAAGTCTCCTGGGGCCCATGATAGCCGTCTTTAACAAGCCCCCT--------------------------TGGGCAGTGAATTAGTTCGCTACGATGCAAGAGTACACACTCCTCATTTGGATAGGCTTGT