Hi
I am trying to run samtools mpileup on a large list of bam files
However, I get a log file which features a list saying
Corresponding, to each of my original input bam files and then a further list of
With a line for each input file.
I have definitely used the samtools sort command to sort these files prior to using mpileup. However, if I use:
I still get a header of @HD VN:1.0 SO:unsorted
So my questions are:
These bam files were intially aligned using bwa and converted from sam to bam with bwa
Thanks in advance for any help
I am trying to run samtools mpileup on a large list of bam files
Code:
samtools mpileup -d 5000 -f /path/to/ref.fa \ /path/to/first.bam \ /path/to/second.bam \ | gzip > output.piledup
Code:
[bam_pileup_core] the input is not sorted (reads out of order [bam_pileup_core] the input is not sorted (chromosomes out of order)
Code:
[bam_plp_destroy] memory leak: 2. Continue anyway.
I have definitely used the samtools sort command to sort these files prior to using mpileup. However, if I use:
Code:
samtools view -H sorted.bam
So my questions are:
- Are my "sorted" bam files actually sorted?
- If they are not, how can I sort them if samtools sort doesn't seem to sort them?
- If they are sorted where else could the error be?
These bam files were intially aligned using bwa and converted from sam to bam with bwa
Thanks in advance for any help
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