When extracting reads aligned to a certain region, what is the difference between using samtools view and bamtools filter region?
Here is the code and the counts of the number of reads recovered. I don't understand why the number of reads recovered are so different between the two approaches. Any help??
samtools index IV75_realigned_reads.bam samtools view -hb IV75_realigned_reads.bam 3R:15,000,000-15,100,000 > Control_region.bam bamtools count -in Control_region.bam # 28034 bamtools filter -region 3R:15,000,000-15,100,000 -in IV75_realigned_reads.bam -out test.bam bamtools count -in test.bam # 7523775