samtools coverage fails to parse the regions

[Lyn16]

Hello,
I am using samtools to get coverage for each chromosome and some specific region.
Here is the code:
samtools coverage -r chr1:1M-12M /Users/lyn/seq_data/WGSdata/tumor_sample_raw_data/Bam/CN9R1_1.final.bam

and error looks like this:

samtools coverage: Failed to parse region "chr1:1M-12M": No such file or directory

I wonder if the problem comes from how I write the specific region? Thanks!

[valeriuo]

The most probable cause is that chr1 does not exist as a contig name in the BAM file header. You can inspect all the contig names with the following command (assuming SN is the 2^nd column) :

samtools view -H /Users/lyn/seq_data/WGSdata/tumor_sample_raw_data/Bam/CN9R1_1.final.bam | grep "^@SQ" | cut -f2

Maybe the chr prefix has been dropped, in which case you should adjust your query to match it:
samtools coverage -r 1:1M-12M ...

However, the error message is misleading and this is on us to fix.

[Lyn16]

Thanks! I checked the contig names with the code you provided, indeed the 'chr' prefix has been dropped in my bam files. And the code is working now