Oxford Nanopore BWA MEM alignments
Hi all,
I have a quick question.
When I run bwa mem for oxford nanopore with the option:
bwa mem -x ont2d
Should I include the option:
bwa mem -x ont2d -M
For split reads? If I want to run Lumpy on the alignments would I need to supply "-M"?
• 4,368 views
•
link
updated
by
WouterDeCoster
•
written
by
QVINTVS_FABIVS_MAXIMVS
•
written
by
QVINTVS_FABIVS_MAXIMVS
1 answer
According to the examples of Lumpy you don't have to use -M:
bwa mem -R "@RG\tID:id\tSM:sample\tLB:lib" human_g1k_v37.fasta sample.1.fq sample.2.fq \
| samtools view -S -b - \
> sample.bam
• 1 views
•
link
written
by
WouterDeCoster
Log in to answer this question.
More posts like this
-
Extracting complete supplementary alignments for long reads from a bam file
written by aacomeau •
-
What are best Long read simulator generating Oxford Nanopore Reads
written by Ashi •
-
Different option in running BWA-MEM
written by nguyenhy258 •
-
Big differences between two alignment tools outputs: BWA vs NanoPipe
written by alexandru.bologa.marian •
-
BWA Mem -M flag (mark split hits) effect on structural variation calling
written by fwuffy
-
BWA MEM Definition of a Primary Alignment
written by QVINTVS_FABIVS_MAXIMVS
-
How does BWA MEM know where to put X and Y origin reads correctly?
written by s1667153 •
-
Can someone explain what the -M option in BWA-MEM does?
written by James Reeve
-
Will the ordering of fasta references influence bwa mem alignment result?
written by hanschen •
-
Are XA: tagged reads == SA: tagged BWAMEM aligned reads?
written by QVINTVS_FABIVS_MAXIMVS
