modkit pileup NEMO_output/dorado_NEMO_mod_aligner.bam NEMO_output/dorado_NEMO_mod_calls.bed
> Error! unable to open SAM/BAM/CRAM index for NEMO_output/dorado_NEMO_mod_aligner.bam; please create an index
modkit can not detect index in bam file. Even I use dorado to basecall it and aligner it ,it does not make any effect.
samtools index NEMO_output/dorado_NEMO_mod_aligner.bam
[E::hts_idx_push] NO_COOR reads not in a single block at the end 0 -1
[E::sam_index] Read '018a0a65-e96c-4157-8e03-5fbcac40b5c6' with ref_name='MT', ref_length=16299, flags=0, pos=9313 cannot be indexed
samtools index: failed to create index for "NEMO_output/dorado_NEMO_mod_aligner.bam": No such file or directory
I want to use samtools to index it, but it also can not work at all
modkit can not detect index in bam file. Even I use dorado to basecall it and aligner it ,it does not make any effect.
I want to use samtools to index it, but it also can not work at all