From 409efe9a3f4a9497f6708b15942e2556900bb4fb Mon Sep 17 00:00:00 2001 From: Sebastian Schoenherr Date: Mon, 18 Jan 2021 15:38:37 +0100 Subject: [PATCH] Update README.md --- README.md | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 5d043c5..dc858e8 100644 --- a/README.md +++ b/README.md @@ -60,15 +60,16 @@ Mutserve allows to annotate the variant file (.txt) with a predefined [annotatio ## Differences to mtDNA-Server -The previous version of mutserve has been integrated in [mtDNA-Server](https://mtdna-server.uibk.ac.at). For scalability reasons, mutserve is parallelized using Hadoop MapReduce but also available as a standalone tool. +The previous version of mutserve has been integrated in [mtDNA-Server v1](https://mtdna-server.uibk.ac.at). +The new changes includes the following changes: - mutserve always reports the non-reference level as the heteroplasmy level, while mtDNA-Server reports the minor component. - mutserve includes a Bayesian model for homoplasmy detection. It uses the 1000G Phase 3 data as a prior and calculates the most likely posterior probability for each genotype. mtDNA-Server only outputs homoplasmic variants with a coverage > 30. ### BAM Preperation -Best Practice Pipelines recommend the following steps for BAM files preperation: -- Local realignment around indels (*GenomeAnalysisTK.jar -T RealignerTargetCreator*, *java -jar GenomeAnalysisTK.jar -T IndelRealigner*) -- BQSR (*GenomeAnalysisTK.jar -T BaseRecalibrator*). +Mutserve is not focused on indel calling. +Best Practice Pipelines include steps for BAM files preperation like local realignment around indels (*GenomeAnalysisTK.jar -T RealignerTargetCreator*, *java -jar GenomeAnalysisTK.jar -T IndelRealigner*) or BQSR (*GenomeAnalysisTK.jar -T BaseRecalibrator*). +Please also have a look at the [Mutect2 Pipeline](https://gnomad.broadinstitute.org/blog/2020-11-gnomad-v3-1-mitochondrial-dna-variants/). ## Output Formats