BAM detect unalign region

Question

[muhammad.zarulhanifah]

Hello folks,

I am running bowtie2 of a sequenced PCR product against a reference allele. Obviously here, my PCR product is bigger than the length of the sequence reads.

How can I detect the presence of unaligned regions/positions early on without visualising on IGV?

Thank you.

Answer 1

[Pierre Lindenbaum]

samtools depth -r "chrom1:234-567" -a in.bam |\
awk '$3=="0" {printf("%s\t%d\t%s\n",$1,int($2)-1,$2);}' |\
sort -t $'\t' -k1,1 -k2,2n |\
bedtools merge