Question: Identification of somatic mitochondrial variants from Ion Torrent data
0
gravatar for Arindam Palodhi
17 months ago by
National Institute of BioMedical Genomics
Arindam Palodhi0 wrote:

Hi,

we have sequenced mitochondrial DNA of BLOOD and TUMOR from oral cancer patients using Ion PGM platform. The inbuilt variant caller produced separate variant call files for blood and tumor data. Our aim is to identify mitochondrial somatic mutations from patients. I have written a tiny code in R to identify variants which are present in tumor only. But so far I am unable to identify heteroplasmic variants which are present in both blood and tumor, but in different frequency.

Ion reporter does not support mitochondrial workflow so we can not go there. Also I have tried varscan2, but it gives a very large number of false indels.

can anybody please suggest  any tool/package/pipeline to solve my problem.

R iontorrent mitochondria • 517 views
ADD COMMENTlink modified 14 months ago by zhaoming1597530 • written 17 months ago by Arindam Palodhi0
0
gravatar for amfkalsbeek
14 months ago by
amfkalsbeek0 wrote:

Hi Arindam,

I had a similar issue and wrote an R script to do just that. If this problem is still unsolved, let me know and I can share the R script with you.

Cheers,

Anton

ADD COMMENTlink written 14 months ago by amfkalsbeek0
0
gravatar for zhaoming159753
14 months ago by
China
zhaoming1597530 wrote:

Hi Anton,

I got the same problem, could you please share your R script for me ? My email is : zhaoming159753@gmail.com Thank you!

Best Regards!

Ming

ADD COMMENTlink written 14 months ago by zhaoming1597530
0
gravatar for zhaoming159753
14 months ago by
China
zhaoming1597530 wrote:

Hi Anton,

I got the same problem, could you please share your R script for me ? My email is : zhaoming159753@gmail.com, Thank you!

Best Regards!

Ming

ADD COMMENTlink written 14 months ago by zhaoming1597530
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