Hello,
I'm having troubles running samtools. When launching the following command:
It ends without error but it only considered the first 3Mbp of the first human chromosome… The results seem to be consistent but very partial (I have reads for all the chromosomes)
If I launch that command
I got the output for all the positions in pileup format, as expected. That is not exactly what I want since there is no SNP calling but that shows mpileup process the whole data.
So, I assume that samtools mpileup is working properly but then why does bcftools stop after a few Mbp? Any idea would be welcome
Thanks!
I'm having troubles running samtools. When launching the following command:
Code:
samtools mpileup -uf ref.fa aln1.bam | bcftools view -bvcg - > var.raw.bcf
If I launch that command
Code:
samtools mpileup -f ref.fa aln1.bam
So, I assume that samtools mpileup is working properly but then why does bcftools stop after a few Mbp? Any idea would be welcome
Thanks!
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