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
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