Which one is the final output?

[biozzq]

Hi,

I have finished a trial for a TGS-based population, but the 05_merge_samples directory contains many files, and which is the final result? Thank you very much.

01.merge_samples.vcf.gz      04.DPinfos.txt              07.filter_raw_vcf_by_depth.vcf.gz  10.thin2.vcf.gz              13.thin2.vcf.gz              15.thin2.indel.vcf.gz  15.thin3.snp.vcf.gz
01.merge_samples.vcfs.list   04.dps                      08.realign0.sorted.vcf.gz          11.realign2.sorted.vcf.gz    14.realign3.sorted.vcf.gz    15.thin2.snp.vcf.gz    15.thin3.sv.vcf.gz
02.realign0.sorted.vcf.gz    05.fill_aug_dp              08.realign0.unsorted.vcf.gz        11.realign2.unsorted.vcf.gz  14.realign3.unsorted.vcf.gz  15.thin2.sv.vcf.gz     15.thin3.vcf.gz
02.realign0.unsorted.vcf.gz  06.merge_samples.vcf.gz     09.thin1.sorted.vcf.gz             12.thin1.sorted.vcf.gz       15.thin1.sorted.vcf.gz       15.thin2.vcf.gz
03.vcf2pos.tsv               06.merge_samples.vcfs.list  09.thin1.unsorted.vcf.gz           12.thin1.unsorted.vcf.gz     15.thin1.unsorted.vcf.gz     15.thin3.indel.vcf.gz

Best wishes, Zheng zhuqing

[starskyzheng]

Hi, zhuqing 15.thin3.vcf.gz contains all final result. PanPop also seprate variants of 15.thin3.vcf.gz by type, which is 15.thin3.snp.vcf.gz, 15.thin3.indel.vcf.gz and 15.thin3.sv.vcf.gz. Hence, all SVs were located in file 15.thin3.sv.vcf.gz.