malformatted region

[txl80]

I am performing straightforward processing of .bam files using the samtools mpileup command. Specifically, these are files generated for the NCI's Cancer Genome Atlas (TCGA) project by Washington University. Most of the files process with no problem, but a large subset of them give the error:

[mpileup] malformatted region or wrong seqname for 1-th input.

The command I am running is exactly:

samtools mpileup -r chr7:55054218-55242525 -uf hg18.fa TCGA-13-0765-01A-01W-0372-09_capture.bam > tmp.pu

I have searched for this error (in seqanswers and Google), but there do not seem to be any prior reports of this behavior.

[sichan]

I ran into the exact same problem just now and the solution was that the chromosome name in my reference fasta fie did not match the sequence name I specified in my region argument (-r). So, I had specified '-r 4:1-191154276' when it should have been 'chr4:1-191154276' since in my reference fasta file, chromosome 4 is represented by 'chr4'

Another potential cause of this error could be that the ordering of chromosomes in your reference fasta file do not match the order that is shown in the BAM file header. All of this is to say that, in my experience, it's best to use the same reference file for aligning and mpileup-ing.

HTH anyone else who has experienced this error.
Simon.

[swbarnes2]

The other quick thing to do is to remake the .bam index. But yes, the most likely cause is that you don't have the chromosome name quite right.