Behaviour with no calls is incorrect

[apeltzer]

Anyways, the bug, or bugs that I found is a very simple one to fix I think. Basically is when you have a T or C as reference and you have no change for that position, so you set as ALT the same nucleotide(normally in vcf format it would be a “.” In the ALT column but inPHAP doesn’t like this, possibly other bug?) . What you will see in inPHAP is for that position is, if you had a “T” it will show a “C” and the other way the same, if you had a “C” as ref it will show a “T”.

Also when representing the case of that a position cant be called (“.|0)”, from my understanding of vcf format, inPHAP makes the call in the opposite allele….

Hope its more or less clear, if not here is a small example that you can upload in inPHAP and see what I mean

##fileformat=VCFv4.1 ##reference=file ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1 Sample2 Sample3 Sample4 geneName1 1 . A G . PASS . GT 0|1 0|1 0|0 0|0 geneName1 35 . G T . PASS . GT 0|1 .|0 0|0 0|0 geneName1 46 . A T . PASS . GT 0|0 0|1 0|0 0|0 geneName1 87 . G C . PASS . GT 0|0 0|1 0|0 0|0 geneName1 117 . T T . PASS . GT 0|0 0|1 .|1 0|0

Look at Sample3 position 117 for the T situation and the how the call for “.|1” is made

And also in Sample3 position 35.