Question

Heteroplasmy detection program

1

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10.3 years ago

mew225 ▴ 20

Hi,

I'm looking for software that detects heteroplasmic variants in mtDNA and have not had much luck. Is there a program works well for calling these variants?

Thanks!

mtDNA • 2.4k views

ADD COMMENT • link updated 3.0 years ago by Ram 44k • written 10.3 years ago by mew225 ▴ 20

Ram · Answer 1 · 2014-07-30

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10.3 years ago

Andreas ★ 2.5k

Shameless plug: you could use LoFreq. It was originally designed for relatively high coverage, low allele frequency data in mind. In the original publication we gave a micro-heteroplasmy example in the context of cancer.

Andreas

ADD COMMENT • link updated 3.0 years ago by Ram 44k • written 10.3 years ago by Andreas ★ 2.5k

Ram · Answer 2 · 2014-07-30

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10.3 years ago

donfreed ★ 1.6k

Have you tried MitoSeek? We have found it pretty easy to work with.

ADD COMMENT • link updated 3.0 years ago by Ram 44k • written 10.3 years ago by donfreed ★ 1.6k

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No I haven't. I'll give it a shot. Thanks!

ADD REPLY • link updated 3.0 years ago by Ram 44k • written 10.3 years ago by mew225 ▴ 20

Ram · Answer 3 · 2016-08-19

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8.3 years ago

haansi ▴ 90

Another shameless plug: you could use mtDNA-Server - it was designed just for this specific task - to determine heteroplasmy in mtDNA ngs data. It also performs a contamination check, based on haplotype / haplogroup checking.

For local usage I can recommend LoFreq - see Andreas answer! Hansi

ADD COMMENT • link updated 3.0 years ago by Ram 44k • written 8.3 years ago by haansi ▴ 90