I am trying to view my exome bam files in IGV, it seems the bam files are too huge (20 GB) each so this is a big constraint to get them viewed in IGV. I got to know that for visualization of large datasets it is useful to convert them to count format or preferably to .tdf format. I have seen the documents and it says this is usually used in case of RNA-Seq and CHIP-Seq. Now the want to use it for exome-seq as well. My data is paired end and with 100bp reads. The coverage is 70X for the samples. How to change the -e parameter for generating the .tdf file for my samples
igvtools count -z 5 -w 25 -e 250 input.bam out.bam.tdf hg19
Can anyone give me suggestions?