Open hasindu2008 opened 1 week ago
Minimap2 would need a -Y in addition to -y I believe in the command below, the supplementary alignments are not hard clipped.
-Y
-y
samtools fastq -TMM,ML test.mod.sam | minimap2 -ax map-ont -y ref.fa - | samtools view -Sb - | samtools sort - > test.aln.mod.bam
Also,
.... | samtools sort - -o test.aln.mod.bam # or .... | samtools sort - > test.aln.mod.bam
would be more efficient.
Minimap2 would need a
-Yin addition to-yI believe in the command below, the supplementary alignments are not hard clipped.Also,
would be more efficient.