how to splice a gene sequence

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There are some sample Individuals with two phenotypes, dwarf and non-dwarf which all are sequenced. I need to splice the SMAD7 gene domain to distinguish whether different phenotypes samples gene have Insertions and deletions.

Only the sequence alignment bam file.

First, I extract fastq file from the bam file and align these with SMAD7 gene to ensure the position of the similar regions.
Second, I extract fastq sequence from the similar regions and assembly it to get SMAD7 gene, then to distinguish whether different phenotypes samples gene have Insertions and deletions.

I failed at the second step, the splice result is poor. The splicing software i used is NOVOPlasty.

Did someone have any suggestions?


assembly

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