Dear Biostars,
I have 45 directories, each containing 2500 bam and 2500 bam.bai files. Each bam file represents alignment results from aligning (shotgun metagenomic) sequences to a reference fasta file. Many of the bam files are empty and only contain the header and no matching/aligned reads. Is there a way to remove these bam files that don't contain matching reads?
Cheers,
Sam
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written
by
samlambrechts299
check with :
find /path/to/dir -type f -name "*.bam" | while read F; do samtools view ${F} | grep -v -E '^@' -m1 > /dev/null || echo $F; done
then replace echo with rm
May I suggest to use samtools view -H ${F} so only the header will be extracted and inspectioned ?
no because there is always a header.
Works perfectly! Thank you!
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