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Question: Question: How to resolve samtools index error "Chromosome blocks not continuous" ?

LEGE
1181 days ago

Question: How to resolve samtools index error "Chromosome blocks not continuous" ?

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.