bed file input for sambamba dept filter outputing unrequested position?

[duartemolha]

Hi

I was using sambamba depth to get the allele counts on my position using an input bed file and I was a bit confused about the output

my bed file contains this position: 4 106155058 106155059

as bed file format is a 0based positional format I am expecting that sambamba would output the basepair numbers on position 106155059 of chromosome 4

whoever the output I get is giving me the counts on the start coordinated of the bed file...

4 106155058 987 987 0 0 0 0 0 Singles-3-NA18527_S3_L001 y

which (assuming sambaba is a 1base positional format ) is not the intended target in the input bed file)

Can you explain?

Many thanks

Duarte

[duartemolha]

Update... Based on the results I am getting it seems sambamba reporting coordinate is 0 base

I used as test a file contaings a range

4 106155050 106155060

REF POS COV A C G T DEL REFSKIP SAMPLE FLAG Processing reference #4 (4) 4 106155050 779 0 0 0 779 0 0 sample y 4 106155051 798 798 0 0 0 0 0 sample y 4 106155052 796 0 0 795 1 0 0 sample y 4 106155053 807 806 1 0 0 0 0 sample y 4 106155054 815 814 0 1 0 0 0 sample y 4 106155055 820 0 0 0 820 0 0 sample y 4 106155056 813 0 0 0 813 0 0 sample y 4 106155057 826 0 826 0 0 0 0 sample y 4 106155058 835 835 0 0 0 0 0 sample y 4 106155059 850 850 0 0 0 0 0 sample y

Based on this we can see the sequence on this region is : TAGAATTCAA

This corresponds to bp position 106155051 .. to ..106155060 (hg19) Translating this to a valid coordinate bed file it would be correctly 4 106155050 106155060

But on the output of sambamba the position indicated by sambamba is off by one (or is 0based)

because for Sambamba the reporting is 4 106155050 106155059

[pjotrp]

Please check the other issues first like #221.