I am trying to use samtools depth (v1.4) with the -a option and a bed file listing the human chromosomes chr1-chr22, chrX, chrY, and chrM to print out the coverage at every position:cat GRCh38.karyo.bed | awk '{print $3}' | datamash sum 13088286401I would like to know how to run samtools depth so that it produces 3,088,286,401 entries when run against a GRCh38 bam file:samtools depth -b $bedfile -a $inputfileI tried it for a few bam files that were aligned the same way, and I get differing number of entries:3087003274308700566630870071583087009435308700943930870096213087009818308701006530870104083087010477308701048130870121153087013147308701318630870135003087149616Is there a special flag in samtools depth so that it reports all entries from the bed file?If samtools depth is not the best tool for this, what would be the equivalent with sambamba depth base?sambamba depth base --min-coverage=0 --regions $bedfile $inputfileAny other options?
samtools depth print out all positions
bam;samtools;sambamba