samtools mpileup -r not working

[tracecakes]

Hi all,

I would like to call SNPs from multiple bam files, one chromosome at a time.

I used the following command to get a vcf file for chromosome 1:

samtools mpileup -Q 20 -q 20 -C 50 -EDIuf canfam3.fasta -r 1 -b bamlist.txt | bcftools view -cg -> chr1.vcf

However it does not work and I get this error message:
[bam_index_load] fail to load BAM index.
[mpileup] fail to load index for 1-th input.
[afs] 0:0.000

After extensive googling, I got a clue that it may work whilst leaving option r out, and it did start to work:

command:
samtools mpileup -Q 20 -q 20 -C 50 -EDIuf canfam3.fasta -b bamlist.txt | bcftools view -cg -> test.vcf

output:
[mpileup] 7 samples in 7 input files
<mpileup> Set max per-file depth to 1142
[bcfview] 100000 sites processed.
[afs] 0:99543.747 1:62.399 2:41.907 3:52.140 4:38.329 5:33.845 6:42.816 7:57.233 8:11.331 9:7.889 10:14.342 11:7.750 12:12.551 13:29.424 14:44.296
[bcfview] 200000 sites processed.
[afs] 0:99754.577 1:37.872 2:35.226 3:81.483 4:18.848 5:8.106 6:3.562 7:6.604 8:1.895 9:4.640 10:12.232 11:4.209 12:4.845 13:8.355 14:17.546

Unfortunately there was no other solutions suggested from that.

Does anyone know why it doesn't work with the "r" option ? I thought the bam files didn't have to be indexed for mpileup... but I still have my original index files (before doing rmdup) anyway.

[lh3]

[bam_index_load] fail to load BAM index.
[mpileup] fail to load index for 1-th input.

You need to run "samtools index yours.bam"

[tracecakes]

Thanks for your reply lh3. I have indexed my bam files and its still not working.

[westerman]

'-r <region>' should work. It works for me. :-) To help in troubleshooting, please do an 'ls -l' of your directory and cat your bamlist.txt file so that we can be sure that you have a good index? Also the first list or two of 'samtools view <one_of_your_files>' so that can be sure that the region names indeed look like '1' instead of something like 'chr1'.