Hi all,
I've been looking into using samtools mpileup to generate coverage. After converting its result to bedgraph format, I've compared it to a self generated one (directly from sam file) and IGVs generated coverage (which is shown with visualisation of sam/bam file). I noticed a small difference in the mpileup and IGVs coverage (and my own which mirrors IGV).
Deletions seems to get coverage from mpileup while IGV does not give them coverage. Technically the base isn't covered by reads which have deletion on them, but on the other hand it "spans" the area by going around it and giving "coverage of deletion" in the sample.
Which way would be better to go with? What do others use?
I've been looking into using samtools mpileup to generate coverage. After converting its result to bedgraph format, I've compared it to a self generated one (directly from sam file) and IGVs generated coverage (which is shown with visualisation of sam/bam file). I noticed a small difference in the mpileup and IGVs coverage (and my own which mirrors IGV).
Deletions seems to get coverage from mpileup while IGV does not give them coverage. Technically the base isn't covered by reads which have deletion on them, but on the other hand it "spans" the area by going around it and giving "coverage of deletion" in the sample.
Which way would be better to go with? What do others use?