AnchorWave icon indicating copy to clipboard operation
AnchorWave copied to clipboard

Published 20 hours ago • verified publisher icon baoxingsong

Lack of understanding of MAF to VCF conversion

Open Deng-Yuan opened this issue 2 years ago • 1 comments

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!

Deng-Yuan avatar Jan 04 '23 14:01 Deng-Yuan

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

shuaiwang2 avatar Jan 05 '23 02:01 shuaiwang2