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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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Error: could not get output VCF file #59

Open Bank-tidy opened 10 months ago

Bank-tidy commented 10 months ago

Hi, Dr. Song Thank you for the development of the software anchorwav！I used your software to successfully generate the maf file, such as ler.anchors,ler.f.maf,ler.log,ler.maf, but unfortunately did not get the vcf file.

This is my ler.log: setupAnchorsWithSpliceAlignmentResult begin reading reference sam begin reading reference sam done reading qry sam begin using parameters detected from the input SAM file for novel anchors identification reading qry sam end setupAnchorsWithSpliceAlignmentResult done! myAlignmentMatchSort done! anchors generate done! AnchorWave done!

This is my scripts:

anchorwave gff2seq -i ${input_dir}/01_data/Col-PEK.gff -r ${input_dir}/01_data/Col-PEK.fa -o ${input_dir}/05_cds_data/Col_cds.fa minimap2 -x splice -t 10 -k 12 -a -p 0.4 -N 20 ${input_dir}/01_data/Col-CC.fa ${input_dir}/05_cds_data/Col_cds.fa > ${input_dir}/05_cds_data/ref_Col.sam minimap2 -x splice -t 10 -k 12 -a -p 0.4 -N 20 ${input_dir}/01_data/Ler-0.fa ${input_dir}/05_cds_data/Col_cds.fa > ${input_dir}/05_cds_data/sam_Ler.sam

anchorwave genoAli -i ${input_dir}/01_data/Col-PEK.gff -as ${input_dir}/05_cds_data/Col_cds.fa -r ${input_dir}/01_data/Col-PEK.fa -a ${input_dir}/05_cds_data/sam_Ler.sam -ar ${input_dir}/05_cds_data/ref_Col.sam -s ${input_dir}/01_data/Ler-0.fa -v ${input_dir}/04_vcf_data/ler.vcf -n ${input_dir}/04_vcf_data/ler.anchors -o ${input_dir}/04_vcf_data/ler.maf -f ${input_dir}/04_vcf_data/ler.f.maf > ${input_dir}/04_vcf_data/ler.log

error: No ler.vcf file had generated in the ${input_dir}/04_vcf_data/

Bank-tidy commented 10 months ago

Since I use your anchorwave to call SV, but tassel converts the format for snp, so I would like to ask if I can generate a VCF file for SV, thank you！

baoxingsong commented 10 months ago

I removed the function to generate VCF file from AnchorWave. You could extract long indel records from the TASSEL GVCF files, if you mean long indel by SV.

Bank-tidy commented 10 months ago

I removed the function to generate VCF file from AnchorWave. You could extract long indel records from the TASSEL GVCF files, if you mean long indel by SV.

Thank you for your reply. So what do you think of my idea of using your previous software version to generate vcf files? Or is it better to use tassel?