第一步
使用pbsv比对
cat id|while read id
do
echo "pbmm2 align --sort -j 12 ~/database/rice/ribenqing/IRGSP-1.0_genome.mmi 01raw/${id}.fq.gz 02pbbam/$id.bam " >>01pbmm2.sh
done
第二步
cat id |while read id
do
echo "pbsv call -j 12 -m 30 ~/database/rice/ribenqing/IRGSP-1.0_genome.fasta 03svsig/$id.svsig.gz 04vcf/$id.vcf" >>04pbcall.sh
done
第三步
cat id |while read id
do
echo "pbsv call -j 12 -m 30 ~/database/rice/ribenqing/IRGSP-1.0_genome.fasta 03svsig/$id.svsig.gz 04vcf/$id.vcf" >>04pbcall.sh
done
群call
pbsv call -j 16 --types INS,DEL,INV,DUP,CNV -m 30 ~/database/rice/ribenqing/IRGSP-1.0_genome.fasta svsig/SRR12451666.svsig.gz svsig/SRR12451667.svsig.gz svsig/SRR12451668.svsig.gz svsig/SRR12451669.svsig.gz svsig/SRR12451670.svsig.gz svsig/SRR12451671.svsig.gz svsig/SRR12451672.svsig.gz svsig/SRR12451674.svsig.gz vcf2/merged1.vcf
