create index bam without having sam file
hi everyone I need to create bam index for variant analysis.but I havenot sam files only bam files avaible.how I can create it? I tried
for i in $(ls $RNA_HOME/alignments/hisat2/*.bam | tr -s '/.' ' ' | awk '{print $(NF-1)}')
do
samtools sort $RNA_HOME/alignments/hisat2/$i.bam > $i.bam
samtools index $i.bam
echo indexing of $i finished
done
and I get an error
[bam_sort_core] merging from 9 files and 1 in-memory blocks...
Thank you for any little help
1 answer
What you see is not an error but just a message telling you that many temporary files have been merged into one, that happens when there is less memory available than the sorting needs so it starts writing tmp files to disk and then merges them. No worries about that. Use ls to see if the bai files are present. In fact only bam files can be indexed with samtools, not sam files. It should be fine.
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