I have an alignment file (
BAM) and an associated index file (
pbi) delivered to me by the sequencing provider. I am trying to visualize the alignments in
IGV (v2.8.0). I first tried to index the (sorted) BAM file using
samtools as follows but it creates an empty index (
samtools index alignment.bam
The resulting index file is essentially empty (16 bytes). Probably as a result, I don't see any information in the alignment track in
FASTA file index, created with
samtools faidx is fine).
IGV doesn't show anything when I indicate that the
pbi file contains the index either.
How can I visualize the alignments?