report only primary alignment BWA-MEM
I can extract primary alignment from sam/bam file using
samtools view -F 260
where 260 = unmapped(4) + secondary alignment(256)
but is there is a way to report primary alignment only for single read in the first place? (-a option in bwa-mem will report all alignment. Is there is option (or way around) so the output file contains the primary aligned read only? )
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Samtools mapped and unmapped flags, what is the difference between the flags?
written by DNAngel
-
Samtools SORT or bedtools bamToFastq giving error when converting reads to fastq.
written by DNAngel
-
Error when trying to convert BAM file to FASTQ.
written by DNAngel
-
Help with Samtools flags to get only primary, unique, non duplicate aligned reads
written by kerem.wainer •
-
Bowtie2 reports no secondary alignments
written by goodez
-
bwa mem algorithm filter secondary alignment
written by xudongyang •
-
Identifying contaminants (cow, pig) in oral rinse exome sequencing data
written by AbiB1 •
-
Secondary Alignment in BAM flag
written by eudoraleer •
-
Ideal samtools view f/F flags
written by by0
-
Why Is Tophat Reporting Secondary Alignments Even When The Option To Do So Is Turned Off
written by Varun Gupta
How about
good, but this do not show any direct way (in bwa-mem itself) to do the job, I still need to depend on another tool
Yes, but is that a problem? I guess you are anyway not using SAM files, right? So one round of samtools is necessary in any case to get binary files.
No, I was searching if there is a flag in bwa-mem to do that directly