I'm using samtools version 0.1.16 (r963:234), bwa 0.6.1-r104 and bowtie 0.12.7 on a Linux box. When I run:
samtools merge file1_672_all.bam file1_672_bowtie.bam file1_672_bwa.bam
I get the following error:
[bam_merge_core] different target sequence name: 'chr8' != 'chrX' in file 'file1_672_bwa.bam'
Both bam files were aligned simultaneously with bwa to the same indexed hg19 fasta files, and no error messages were printed during execution.
How can I find out what has gone wrong? Has anyone else come across this problem before? The only other thread that I came across with this error had something to do with joining chromosome-separated bam files together before trying to merge them with samtools.
This didn't happen with a very small dataset I've run through the alignment/variant calling process in this pipeline, so I have seen the setup work previously.
Thank you much.
samtools merge file1_672_all.bam file1_672_bowtie.bam file1_672_bwa.bam
I get the following error:
[bam_merge_core] different target sequence name: 'chr8' != 'chrX' in file 'file1_672_bwa.bam'
Both bam files were aligned simultaneously with bwa to the same indexed hg19 fasta files, and no error messages were printed during execution.
How can I find out what has gone wrong? Has anyone else come across this problem before? The only other thread that I came across with this error had something to do with joining chromosome-separated bam files together before trying to merge them with samtools.
This didn't happen with a very small dataset I've run through the alignment/variant calling process in this pipeline, so I have seen the setup work previously.
Thank you much.
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