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baoxingsong / AnchorWave

Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation
MIT License
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Lack of understanding of MAF to VCF conversion #40

Open Deng-Yuan opened 1 year ago

Deng-Yuan commented 1 year ago

It is a bit difficult to use MAFToGVCFPlugin to convert MAF files to VCF. Is there any other way to convert MAF to VCF? I lack a certain understanding of docker!

shuaiwang2 commented 1 year ago

thanks for your questions. Convert MAF file to VCF file with tassel is the best way. The plugin can run directly from tassel-5-standalone as follow. this is an example to maize :

/home/xuql/tassel-5-standalone/run_pipeline.pl -Xmx100G -debug -MAFToGVCFPlugin -referenceFasta /home/xuql/copyNAM/B73/Zm-B73-REFERENCE-NAM-5.0.fa -mafFile /home/xuql/copyNAM/B97/B97.maf -sampleName B97_anchorwave -gvcfOutput /home/xuql/copyNAM/B97/B97ToB73.gvcf -fillGaps false > /home/xuql/copyNAM/B97/B97_outputMafToGVCF.txt