DP4 in the VCF File (enhancement) ?

mitoNGS / MToolBox

A bioinformatics pipeline to analyze mtDNA from NGS data

http://sourceforge.net/projects/mtoolbox/?source=navbar

GNU General Public License v3.0

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DP4 in the VCF File (enhancement) ? #61

Closed 3i-v closed 5 years ago

3i-v commented 6 years ago

Is it possible to add the strand bias (DP4) into the VCF info field ? Thank you, v.

Confurious commented 6 years ago

yeah, this is very much needed for calling mitochondria variants, and is available from mt-DNA server

clody23 commented 5 years ago

Hi,

yes, this is indeed an improvement we are planning to do in the next version of the tool we are currently working on.

Best regards, Claudia

clody23 commented 5 years ago

We have released version 1.2 version of MToolBox that supports the calculation of the read depth per strand of the ALT allele only. This is now reported as an additional field in the VCF (SDP).