Complex Variant Calling
BWA-MEM aligns any previously generated FASTQ files to a complex variant reference sequence data set. The data set represents 29 complex indels of the EGFR gene. The complex variant caller uses EGFR variant reference sequences for the following tasks.
| • | Creating alternative alignments and performing duplicate marking on the resulting alignments |
| • | Comparing the alternative alignments to variant calls to determine whether an EGFR complex variant is present |
The complex variant caller sorts and indexes the data set, flagging duplicate reads in BAM files and generating BAM files with alignments and indexes. The complex variant caller then calls complex variants in the BAM files and generates a variant call file.