I'm trying to align some Illumina amplicon sequencing, generated on a MiSeq, using Rsubread. It outputs .bam, .indel.vcf, and .summary files, but no .bai file, so I can't display the results in IGV. Here's how I got to this point:

1. Download the chr5.fa.gz reference sequence from UCSC (https://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/).

2. Create an index using: buildindex(basename="reference.ch5", reference="chr5.fa")

3. Align my paired end sequencing files:

reads1.ch5 <- file.path(dirPath, "MSH3repeat_S1_L001_R1_001.fastq.gz")

reads2.ch5 <- file.path(dirPath, "MSH3repeat_S1_L001_R2_001.fastq.gz")

align(index="reference.ch5", readfile1=reads1.ch5, readfile2=reads2.ch5, output_file="alignResults.ch5.BAM")

How do I get it to make a .bai file, and how do I then display the results in IGV? Thanks!

bai files are only produced when reads are sorted by genomic position, which Rsubread::align will do if you set sortReadsByCoordinates = TRUE.

Rather than running align again, you could use samtools to sort the bam files. That does not require re-alignment.