Hi, many thanks for replying. It's now much clearer what these parameters mean, but I still have a question. I generated the VCF I showed above using one sample A, targeting on a region on Chr12. I used the codes:
Construct graph and index (according to whole genome variation graph)
echo constructing graph
(seq 1 21; echo X; echo MT) | parallel -j 23 "time vg construct -C -R {} -r $ref -v $vars -t 1 -m 32 > $dir/{}.vg"
vg ids -j $(for i in $(seq 1 21; echo X; echo MT); do echo $i.vg; done)
vg index -x wg.xg $(for i in $(seq 1 21; echo X; echo MT); do echo $i.vg; done)
for chr in $(seq 1 21; echo X; echo MT);
do
vg prune -r $chr.vg > $chr.pruned.vg
done
vg index -g wg.gcsa $(for i in $(seq 21; echo X; echo MT); do echo $i.pruned.vg; done)
Map and call variant (according to Whole genome calling and genotyping)
vg map -x $dir/wg.xg -g $dir/wg.gcsa -f $fastq/A_R1.fastq.gz -f $fastq/A_R2.fastq.gz > $dir/A.gam
vg gamsort $dir/A.gam -i $dir/A_sorted.gam.gai > $dir/A_sorted.gam
vg chunk -x wg.xg -c 10 -p 12:20140000-23600000 -g -a A_sorted.gam -O pg > A_sorted_chunk.pg
vg augment A_sorted_chunk.pg A_chunk_0_12_20139664_23600147.gam -s -A A_final.gam > A_final.pg
vg snarls A_final.pg > A_final.snarls
vg pack -x A_final.pg -g A_final.gam -o A_final.pack
vg call A_final.pg -r A_final.snarls -k A_final.pack -s sample > sample_calls.vcf
Everything went fine, except from the POS in the VCF seems not to be the coordinates along the Chr12. The POS should be around this 12:20,140,000-23,600,000 region...
Did I do something wrong in the code by missing some parameters? Thanks in advance.
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