how to map reads and get bam for manta

[YaqiangCao]

Dear developer, I am quite new in this field. My purpose was to check if the genome has integrated one specific sequence and where the sequence are. So I think the insert should be called with manta output with "MantaINS" ids. I am quite curious which is the right way to prepare bam files, following are my method, please let me know if this is not right with bwa's soft clipping mapping.

bwa mem -Y -M -t 20 mm10.fa test_R1.fastq test_R2.fastq >  test.sam

The sam file was converted to bam, sorted and indexed, wanta was run successfully, however, I did not find any target insertion. 

Thanks. 

Best, Yaqiang