Heteroplasmy detection program
3 answers
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
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
Log in to answer this question.
More posts like this
-
Best way to do protein structure guided similarity search?
written by Mark •
-
BCFtools for somatic vs. germline variant calling
written by rebeliscu •
-
MUtect2-Vardict
written by sarastrafella.ss •
-
Count variants between two samples within a multi-sample VCF
written by rc16955
-
Regarding Human Exon Variant Reference
written by k.manojkumar2991 •
-
Alignment plot of a small extract (sequence) from a .bam file
written by Michi
-
Chip-Seq - Peak caller for broad enrichment of histone modifications?
written by ej
-
Interpretation of InDels obtained from the Freebayes variant caller on Mitochondrial DNA
written by mew225 •
-
Comparison between .bam files
written by mew225 •
-
Y Chromosome Haplotype Inference
written by Vivek
