Dear all,
I am having some strange issues with samtools mpileup. I am running exactly the same command using either:
-r 17:45249328-45249329
or
-l chr17c.bed
where chr17c.bed is a one line BED file:
17 45249328 45249329
The latter, which uses a bed file, is incredibly slow. We also seem to observe a bug at some rare locations of the genome but we haven't gotten to the bottom of this.
Is there a real difference between using -l or -r? Why do I observe a different behavior? Can anyone give me dome details on the way samtools works in this case?
Thank you in advance, and happy to provide more details if it helps,
Vincent
PS: the full command line looks like
samtools mpileup -ugf /ugi/home/shared/vincent/reference_genome/fasta/human_g1k_v37.fasta -D -l chr17c.bed -b my_220_bamfiles.tab
I am having some strange issues with samtools mpileup. I am running exactly the same command using either:
-r 17:45249328-45249329
or
-l chr17c.bed
where chr17c.bed is a one line BED file:
17 45249328 45249329
The latter, which uses a bed file, is incredibly slow. We also seem to observe a bug at some rare locations of the genome but we haven't gotten to the bottom of this.
Is there a real difference between using -l or -r? Why do I observe a different behavior? Can anyone give me dome details on the way samtools works in this case?
Thank you in advance, and happy to provide more details if it helps,
Vincent
PS: the full command line looks like
samtools mpileup -ugf /ugi/home/shared/vincent/reference_genome/fasta/human_g1k_v37.fasta -D -l chr17c.bed -b my_220_bamfiles.tab
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