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.
[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.
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