Max depth 8000
LauraVP1994 opened this issue · 1 comments
Dear,
Althought this would be a great tool, I encountered quite a big problem for my data with bam-read-count. Just like samtools depth it seems not to deal well with high coverages. I have coverages ranging from 5000-90 000X and bamreadcount seems to limit itself to 8000. I found a few posts that tried to deal with this with the -d option. However this doesn't seem to work.
Maybe an update or a clear workaround is necessary for people that work with high coverages like viral data.
Kind regards
Laura
I was able to get this to work as follows up to 10,000,000x depth (I think the default). This may require both the reference FASTA and the segment at the end.
# filter bases at Q30
bam-readcount -b 30 -w 1 -f $REFERENCE my.sorted.bam chrID
EDIT: I highly recommend the -w 1
option to limit potential warnings, otherwise you can get a flood. It does take a while to plow through ultra high coverage data (guessing from dealing with the huge pileup).