How To Find Reads With Secondary Alignment In Bwa Mem Sam File ?
In BWA MEM sam is there any tag that represents reads having secondary alignment? How to find reads with secondary alignment?
As XA tag represents Secondary alignment for aln command. But how to find in BWA MEM?
• 9,541 views
•
link
updated
by
Ram
•
written
by
Samarth Kulshrestha
•
written
by
Samarth Kulshrestha
2 answers
use
samtools view -f (flag) file.bam
with flag=not primary alignment http://picard.sourceforge.net/explain-flags.html
• 96 views
•
link
written
by
Pierre Lindenbaum
Thanks for response. When i am using flag 2048 (supplementry alignment) , MEM output is showing results reads with SA tags ie chimeric alignment.
But in case in case i am interested in secondary alignment then what i need to do? shall i use flag 256 (not primary alignment)??
• 0 views
•
link
written
by
Samarth Kulshrestha
Log in to answer this question.
More posts like this
-
Multimapping artefacts in variant calling
written by ashakru •
-
Listing of actual Alignmentes mentioned by BWA MEM XA tag version 0.7.17
written by kmzhou4 •
-
bwa mem and multiply mapped reads
written by lfreeborn •
-
very-sensitive-local bowtie2 or bwa_mem
written by Illusion •
-
bwa XA field: What is the procedure for the binning of all but one alternative alignments into XA?
written by izaak.coleman1 •
-
bwa mem algorithm filter secondary alignment
written by xudongyang •
-
BWA barcode trimming and labeling
written by igor
-
bwa aln for paired-end sequencing data in one .fastq file
written by ciemanek
-
Are XA: tagged reads == SA: tagged BWAMEM aligned reads?
written by QVINTVS_FABIVS_MAXIMVS
-
bwa-0.7.12 AS:i and XS:i match but MAPQ = 0
written by suzanne.mcgaugh
