I'm running samtools v1.18 on macOS/arm64
I have a dataset of very high coverage data, when running
samtools bedcov -c -g SECONDARY,QCFAIL,DUP $BED $BAM
it reports the number of reads in one interval as 1,300,694. However,
samtools view -c -F UNMAP $BAM $REGION
reports 6,277,273 which is significantly different. bedtools coverage also reports 6,277,273. Through trial and error, I discovered that
samtools bedcov -c -d 1000000 -g SECONDARY,QCFAIL,DUP $BED $BAM
reports 6,277,273. Different values for -d results in a number of reads reported between the 1.3M and 6.2M. My question is, is this a bug in bedcov when processing very high coverage data or a feature that's limiting the number of reads under some circumstances? It's not obvious to me at all why the -d option would change the total number of reads reported, and, if this isn't a bug, how can I ensure that the total number of reads is always reported (-d 1000000 worked for one particular BAM but might not universally work)?
Thanks
I'm running samtools v1.18 on macOS/arm64
I have a dataset of very high coverage data, when running
it reports the number of reads in one interval as 1,300,694. However,
reports 6,277,273 which is significantly different.
bedtools coveragealso reports 6,277,273. Through trial and error, I discovered thatreports 6,277,273. Different values for
-dresults in a number of reads reported between the 1.3M and 6.2M. My question is, is this a bug inbedcovwhen processing very high coverage data or a feature that's limiting the number of reads under some circumstances? It's not obvious to me at all why the-doption would change the total number of reads reported, and, if this isn't a bug, how can I ensure that the total number of reads is always reported (-d 1000000worked for one particular BAM but might not universally work)?Thanks