Question: Alignment with BWA: how to discard multi mappers?
0
gravatar for ThePresident
3.5 years ago by
ThePresident140
ThePresident140 wrote:

Hello,

This topic has been discussed on many occasions however I couldn't find the right answer afterall.

I am aligning Illumina generated paired-end reads on reference genome with BWA. My understanding is that when BWA finds multiple equally perfect alignments for one read, it will report/map that read randomly. However, I couldn't find an option for discarding these reads, i.e. similar to -m1 option from bowtie (there is a specific reason why I want to use bwa over bowtie).

Did I miss something or...?

Thanks

bwa paired-end • 1.7k views
ADD COMMENTlink modified 3.5 years ago by igor9.6k • written 3.5 years ago by ThePresident140

You can screen the bam file afterwards for reads with no other hits.

ADD REPLYlink written 3.5 years ago by Asaf7.0k
0
gravatar for igor
3.5 years ago by
igor9.6k
United States
igor9.6k wrote:

There is no parameter you can use, but you can filter the BAM with samtools. See this previous discussion: BWA mem how to know if a read is mapped uniquely? and Bwa-Mem: Discriminate Between Reads Mapping Uniquely And Those Mapping In Multiple Positions

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by igor9.6k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1518 users visited in the last hour