samtools index mappedPairs.sorted.bam return the following error ...
[bam_sort_core] merging from 0 files and 2 in-memory blocks... [E::hts_idx_push] Chromosome blocks not continuous samtools index: failed to create index for "mappedPairs.sorted.bam"
Answers
0
It generally occur when you sort with -n flag (-samtools sort n /Sort by read name). Try sorting without -n flag and then index it.
It generally occur when you sort with -n flag (-samtools sort n /Sort by read name). Try sorting without -n flag and then index it.