merging bam files with different headers

dnusol · 02-06-2012, 08:05 AM

Hi,

Is it possible to merge bam files from the same sample but different reference sequence and thus different headers, so that I work with one single alignment file instead of two?.

I tried

Code:

java -Xmx4g -jar ~/picard-tools-1.61/MergeSamFiles.jar  INPUT=Sample1_exon1.bam INPUT=Sample1_exon2.bam OUTPUT=Sample1_merged.bam ASSUME_SORTED=true USE_THREADING=true VALIDATION_STRINGENCY=LENIENT

but I got the following error:

Exception in thread "main" net.sf.samtools.util.SequenceUtil$SequenceListsDifferException: Sequences at index 0 don't match

Cheers,

Dave

p.s.: I must say that the MERGE_SEQUENCE_DICTIONARIES flag seems to be related to this task but I am not sure what it actually means

Richard Finney · 02-06-2012, 08:13 AM

Even it if were possible, it wouldn't be a good idea.

Check samtools merge documentation at http://samtools.sourceforge.net/samtools.shtml

merge samtools merge [-nur1f] [-h inh.sam] [-R reg] <out.bam> <in1.bam> <in2.bam> [...]

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.

dnusol · 02-07-2012, 12:09 AM

Thanks Richard,

I was afraid of that. I see it as doing two steps of alignment against two different reference files instead of doing one single alignment against a file with two fasta entries. I guess the issue here is that you loose the ability of finding reads if multiple alignment is taking place. Unless this is done in a late step. But why a bad idea? to me it seems just a technical issue (samtools will only take into account headers of first in.bam file)

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02-06-2012, 08:05 AM	#1
dnusol Senior Member Location: Spain Join Date: Jul 2009 Posts: 133	merging bam files with different headers Hi, Is it possible to merge bam files from the same sample but different reference sequence and thus different headers, so that I work with one single alignment file instead of two?. I tried Code: java -Xmx4g -jar ~/picard-tools-1.61/MergeSamFiles.jar INPUT=Sample1_exon1.bam INPUT=Sample1_exon2.bam OUTPUT=Sample1_merged.bam ASSUME_SORTED=true USE_THREADING=true VALIDATION_STRINGENCY=LENIENT but I got the following error: Exception in thread "main" net.sf.samtools.util.SequenceUtil$SequenceListsDifferException: Sequences at index 0 don't match Cheers, Dave p.s.: I must say that the MERGE_SEQUENCE_DICTIONARIES flag seems to be related to this task but I am not sure what it actually means Last edited by dnusol; 02-06-2012 at 08:14 AM.

02-06-2012, 08:13 AM	#2
Richard Finney Senior Member Location: bethesda Join Date: Feb 2009 Posts: 700	Even it if were possible, it wouldn't be a good idea. Check samtools merge documentation at http://samtools.sourceforge.net/samtools.shtml merge samtools merge [-nur1f] [-h inh.sam] [-R reg] <out.bam> <in1.bam> <in2.bam> [...] 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.

02-07-2012, 12:09 AM	#3
dnusol Senior Member Location: Spain Join Date: Jul 2009 Posts: 133	Thanks Richard, I was afraid of that. I see it as doing two steps of alignment against two different reference files instead of doing one single alignment against a file with two fasta entries. I guess the issue here is that you loose the ability of finding reads if multiple alignment is taking place. Unless this is done in a late step. But why a bad idea? to me it seems just a technical issue (samtools will only take into account headers of first in.bam file)