I have been working with several tools on bam files recently and I am not sure how I should interpret some of the outputs.
samtools idxstats mapped.sorted.bam
Chr1 15096 0 0 Chr2 33397 0 0 Chr3 43888 41 0 Chr4 20819 1 0 * 0 0 34
Documentation says third and fourth column give "mapped reads" and "unmapped reads". So I interpreted the last line (
*) as the number of unmapped reads as this is the only line with a non 0 value at this field.
Then I used
bam splitChromosome --in mapped.sorted.bam --out test/aln.
Reference Name: chr6 has 6 records Reference Name: Chr7 has 1 records Reference Name: Chr3 has 41 records Reference Name: Chr4 has 1 records Reference Name: * has 34 records
And looking at the bams outputted (one per reference sequence) in
test/ I find an
aln.UnknownChrom.bam that I am not sure where it comes from. I actually found 97 unique reads ID in it, where I was waiting for 34 or less.
So my first question is : Does "*" actually means "all reads that didn't mapp" and this information is stored in way I didn't know about in BAM files ?
And my second question would be : Anybody knows where this
aln.UnknownChrom.bam comes from when using
splitChromosome ? It is a source of error in a pipeline I am building and I'd like to get rid of it, if these are not actual mapping informations.