2026-04-21

awk 'BEGIN{OFS="\t"} /^P/{$2=$2"#1#chr01"} 1' binary.pg.full.gfa > binary.pg.full.renamed.gfa
vg convert -g -p   binary.pg.full.renamed.gfa  > binary.pg.full.renamed.vg
 vg mod -X 32  binary.pg.full.renamed.vg  > binary.pg.full.renamed.chop32bp.vg
vg clip binary.pg.full.renamed.chop32bp.vg   -d 5 -P ref -m 1000 | vg clip -d 1 - -P ref | vg clip -sS - -P ref  > binary.pg.full.renamed.chop32bp.d5.vg
vg convert -f binary.pg.full.renamed.chop32bp.d5.vg > binary.pg.full.renamed.chop32bp.d5.gfa
vg autoindex -p mapping.d5 -g binary.pg.full.renamed.chop32bp.d5.gfa    -w giraffe -t 5

# 
vg giraffe -t 10 -p -Z 97samples.giraffe.gbz -m 97samples.min -d 97samples.dist \
    -f 1803_1.fq.gz -f 1803_2.fq.gz \
    1>1803.gam 2>1803.gam.log
(vg filter 1803.gam -r 0.90 -fu -m 1 -q 15 -D 999 -t 2 -x \
    97samples.full.chop.32.d10.xg | \
    vg view -aM - | nodegwas count -n 1803.filter.node) 1>AH1803.filter.node.log 2>&1
nodegwas rmerge -i sample.list -o node_table -n 2 -t

# here, make sure We got nodetable.gz file, 
![image.png](https://upload-images.jianshu.io/upload_images/27226870-4068b27455ad40dc.png?imageMogr2/auto-orient/strip%7CimageView2/2/w/1240)

nodegwas extract  -g binary.pg.full.renamed.chop32bp.gfa -n node.source
nodegwas tovcf -k  nodetable.gz -n node.source