Question: CNV tools for mitochondrial chromosome using whole-genome sequencing
0
gravatar for hellbio
2.5 years ago by
hellbio330
hellbio330 wrote:

Could someone suggest any tools that work well for mitochondrial cnv detection using whole-genome sequencing data? Thanks!!

cnv chrmt • 1.0k views
ADD COMMENTlink modified 2.5 years ago by QVINTVS_FABIVS_MAXIMVS2.1k • written 2.5 years ago by hellbio330
0
gravatar for QVINTVS_FABIVS_MAXIMVS
2.5 years ago by
USA SoCal
QVINTVS_FABIVS_MAXIMVS2.1k wrote:

If you want to find mitochondrial insertions INTO the human genome DINUMT

For SV in the mitochondria genome I know Manta and possibly lumpy (I don't have raw lumpy output at hand right now) will call SVs within the mitochondria

You might want to look into INDEL callers too since you do not expect to see a SV >5kb in the mitochondria. Haplotype Caller, FreeBayes, Platypus, and Scalpel are programs my lab works with (not me personally)

ADD COMMENTlink written 2.5 years ago by QVINTVS_FABIVS_MAXIMVS2.1k
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: 811 users visited in the last hour