I'm trying to get read counts of a region that I see in IGV has around 2k read counts. When I use samtools I get 10x more. The number that it's very similar to the level of read counts for exons in this region.
How to get a number of reads for this intronic region from the Terminal?
~ samtools view -c MEX_WT_7Aligned.sortedByCoord.out.bam VII:439190-439190
24029
IGV using default parameters removes supplementary reads, duplicates, failing QC, etc... check this using the
-f/-F
option of samtools view