[E::hts_idx_push] Unsorted positions on sequence tbx_index_build failed:

tabix构建索引

tabix -p vcf test.vcf.gz

报错

[E::hts_idx_push] Unsorted positions on sequence #1: 130023 followed by 130022

tbx_index_build failed: test.vcf.gz

分析

由以上可以知道，错误是由test.vcf.gz中变异未能按照染色体、位置排序导致

解决

重新排序

less test.vcf|grep -v '#'|sort -k1,1d -k2,2n >body
less test.vcf|grep '^#' >header
cat header body >test1.vcf

重新索引即可