Assembly on scaffold level

Open Meer9234 opened this issue 2 years ago • 0 comments

Hi,

Can I also use this tool when I have a reference genome on scaffold level? And how do I do the samtool mileup then (and the rest)? Because the samtools mileup is running for a long time >2 days with 128 cores. My assembly is 1.3GB. I used this command: bcftools mpileup -Q 30 -q 30 -f $REFERENCEFA $ALIGNMENTS -o $OUTBCFMPLIEUP

Kind regards

Oct 13 '23 16:10 Meer9234