If you only want to exclude telomeres, which are at the ends of chromosomes, you can write a simple script to get the complement of the regions. For more complex regions, you can use bedtools to get the complement of regions.
Once you have BED, you can use "view -L in.bed" to pull the alignments you want.
Heng
I have whole genome alignment bam file (from human genome) and I want to exclude all the reads aligned to centromeric and telomeric regions. I already have coordinates for those regions. Is there anyway to do it using Samtools. The data is paired-end read data.
Thanks.
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Vinay Kumar Mittal
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