Closed socialhang closed 1 year ago
This is our pipeline for the MAFToGVCFPlugin
https://github.com/baoxingsong/AnchorWave/blob/master/doc/GATK.md . If it does not work for you, could you please share your data and all the commands?
Thanks for your reply!
This is my command and data.
anchorwave gff2seq -i chr1.1.raw.small.gff -r raw_chr1.1.small.fa -o chr1.1.cds.fa
minimap2 -x splice -t 40 -k 12 -a -p 0.4 -N 20 new_chr1.1.small.fa chr1.1.cds.fa > new_chr1.1.sam
minimap2 -x splice -t 40 -k 12 -a -p 0.4 -N 20 raw_chr1.1.small.fa chr1.1.cds.fa > raw_chr1.1.sam
anchorwave genoAli -t 40 -v -i chr1.1.raw.small.gff -as chr1.1.cds.fa -r raw_chr1.1.small.fa -a new_chr1.1.sam -ar raw_chr1.1.sam -s new_chr1.1.small.fa -n align.anchors -o alignment.maf -f alignment.f.maf
run_pipeline.pl -Xmx76G -debug -MAFToGVCFPlugin -referenceFasta raw_chr1.1.small.fa -mafFile alignment.maf -sampleName chr1.1 -gvcfOutput runpip.gvcf -fillGaps false
Hi,@baoxingsong:
I'm sorry to bother you again. Do you have some results about my data?
best wishes!
data.tar.gz I renamed your chromosomes, it worked. I did not write code of the TASSEL part, and have no idea why that happen. I will forward this message to my TASSEL colleagues.
Thanks!!!
Hi, @baoxingsong :
I had this error in MAFToGVCFPlugin:
[pool-1-thread-1] ERROR net.maizegenetics.plugindef.AbstractPlugin - GenomeSequenceBuilder.chromosomeSequence: chromosome not found
what should I do for my MAF format?