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I start with the command: samtools faidx reference.fasta. This results in the reference.fasta file going from 120 MB to a reference.fasta.fai file of 4 KB size on disk, but a size of 264 bytes.
Then I give this command: samtools view -bS -t reference.fasta.fai alignment.sam -o alignment.bam
This results in a scrolling screen with lines that all are variants of: [sam_read1] reference 'chr1.fa' is recognized as '*'.
Where the variation in the lines are just in the chromosome number, chr2.fa, chr5.fa etc.
Something seems to be not correct in this ?
Then I give this command: samtools view -bS -t reference.fasta.fai alignment.sam -o alignment.bam
This results in a scrolling screen with lines that all are variants of: [sam_read1] reference 'chr1.fa' is recognized as '*'.
Where the variation in the lines are just in the chromosome number, chr2.fa, chr5.fa etc.
Something seems to be not correct in this ?