I merged several bam files into a merged one (merged_bam) and used it as input to lumpy. The original bam files have different names (RG:Z flag) and the output vcf file contains only one of them in the sample name. I wonder if I need to change the RG:Z flag to be the same in the merged_bam before running lumpy (so that it would use all the reads). Or does it already use all the reads and choose one of the RG:Z flags for the output vcf?
Hi Teams,
I merged several bam files into a merged one (merged_bam) and used it as input to lumpy. The original bam files have different names (RG:Z flag) and the output vcf file contains only one of them in the sample name. I wonder if I need to change the RG:Z flag to be the same in the merged_bam before running lumpy (so that it would use all the reads). Or does it already use all the reads and choose one of the RG:Z flags for the output vcf?
Thanks! Mark