I have two (or more) .bam files for same sample... I want to merge them in to one bam file. Which I tired with samtools merge command. But in the output file I have different SM codes and both are in that file. The
samtools merge out.bam in1.bam in2.bam in3.bam
@RG ID:N15 PL:ILLUMINA SM:N15
@RG ID:N17 PL:ILLUMINA SM:N17
@PG ID:bwa PN:bwa VN:0.6.1-r104-tpx
@PG ID:bwa-59218C57 PN:bwa VN:0.6.1-r104-tpx
When I use this file in my pipeline for generating g.vcf files, the walker haplotypecaller is not working due to different sample names. How can I overcome this?