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  • samtools mpileup -r not working

    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.

  • #2
    [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"

    Comment


    • #3
      Thanks for your reply lh3. I have indexed my bam files and its still not working.

      Comment


      • #4
        '-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'.

        Comment

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