Issues with the input file

[jwli-code]

In your README file, it is recommended to directly use BAM files from second-generation sequencing and third-generation sequencing. However, my second-generation BAM files are generated using BWA alignment. I’m not sure if this will have any impact. craq -g assembly.fa -sms SMS_sort.bam -ngs NGS_sort.bam

[JiaoLaboratory]

Thank you for using CRAQ! CRAQ also supports second-generation sequencing BAM files generated using BWA alignment, so this will not affect the analysis results.