Samtools error: "different target sequence name"

[evansdan]

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.

[swbarnes2]

You didn't mention that the .bam files were sorted. Do your files conform to what the documentation says they have to look like?

Merge multiple sorted alignments. The header reference lists of all the input BAM files, and the @SQ headers of inh.sam, if any, must all refer to the same set of reference sequences. The header reference list and (unless overridden by -h) ‘@’ headers of in1.bam will be copied to out.bam, and the headers of other files will be ignored.

http://samtools.sourceforge.net/samtools.shtml

[spacup]

Yes, sure. But how to do when you want to merge a .bam file generated from a male sample with another one generated from a female sample?

Just add the ChrY line in the female header .bam file ?
The problem is that .bam are compressed binary files... so how to do?

See thread : http://seqanswers.com/forums/showthr...153#post126153