BWA Mem -M flag (mark split hits) effect on structural variation calling
2
4
Entering edit mode
5.1 years ago
fwuffy ▴ 110

Does anyone know if BWA Mem -M flag (mark shorter split hits as secondary) will have a detrimental effect on structural variation calling using split reads with Delly?

I orignially added it to my BWA mapping pipeline for compatibility with Picard/GATK but I believe that issue has been resolved in GATK4. Now wondering if it's even necessary and if it will have an effect on SV calls that use split reads.

Input to this pipeline may include paired, single end, interleaved or split data from illumina, ion torrent, or nanopore.

bwa structural-variations delly • 2.7k views
ADD COMMENT
4
Entering edit mode
5.1 years ago
trausch ★ 1.9k

For delly, it doesn't make a difference if split reads are marked as secondary or supplementary.

ADD COMMENT
4
Entering edit mode
5.1 years ago
Vitis ★ 2.6k

I've never used -M option for structural variant calling. Based on this BWA thread, you may lose supplementary mapping information by using -M option, because -M may label split reads as duplicates and strip the secondary/supplementary mapping information. I believe at least some SV tools use split read information for variant calling.

https://github.com/lh3/bwa/issues/163

The best way might be to try running a small experiment of calling SVs with and without -M option to see the differences.

ADD COMMENT

Login before adding your answer.

Traffic: 2818 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6