Question: detect large indels
0
gravatar for nakanomasayuki265
2.5 years ago by
nakanomasayuki26560 wrote:

What is the best way to detect large indels ? I mapped reads of whole genome shotgun sequencing against the reference sequences.

sequencing • 1.4k views
ADD COMMENTlink modified 2.5 years ago by Brian Bushnell16k • written 2.5 years ago by nakanomasayuki26560
4
gravatar for Brian Bushnell
2.5 years ago by
Walnut Creek, USA
Brian Bushnell16k wrote:

The best way to detect large deletions is to map with BBMap and call variants with the BBMap package's CallVariants tool. BBMap can also detect moderate-sized insertions (up to 60% of insert size, or so). For example:

bbmap.sh in=reads.fq out=mapped.sam ref=ref.fa maxindel=400k
callvariants.sh in=mapped.sam out=vars.vcf ref=ref.fa ploidy=2

For longer insertions that cannot be captured within a read pair it's probably better to use an indel-specific caller based on coverage and read pairing. But for insertions shorter than ~60% of insert size it's better to merge reads, map them, and call them with a normal variant-caller. I've used BBMerge -> BBMap -> CallVariants successfully with >200bp insertions from 2x100bp reads.

Note that I wrote BBMap and I am biased.

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by Brian Bushnell16k
1
gravatar for 2nelly
2.5 years ago by
2nelly170
Geneva,Switzerland
2nelly170 wrote:

Some good tools are:

https://github.com/dellytools/delly

https://github.com/zeeev/wham

https://github.com/arq5x/lumpy-sv

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by 2nelly170
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