Inconsistent output when run with or without bed file for regions

[juliandangelo]

I am currently trying to use the bam-readcount program to look at allelic frequencies and distributions at specific locations. When running the command with a bed file (tab-separated), I am not seeing the same insertion and/or deletion events as when ran with the specific regions from a piped echo command.

For example:

echo -e 17\t7570000\t7571000 | bam-readcount -w 0 -q 1 -b 20 -l /dev/stdin -f $reference $inBAM

&

bam-readcount -w 0 -q 1 -b 20 -l $bedFile -f $reference $inBAM

The difference is that sometimes the the deletion/insertion event/s are not listed at all in the output file which used a bed file as the region input. I found that running the command in a loop, parsing each line in the bed file and passing that through the first example command works as intended, but running the bottom example command where the bed file is the input regions does not work as intended.