VCF mods

[iqbal-lab]

Right, v quick github issue before i fly to freedom

Current VCF looks like this (sorry looks horrid in github markdown)

##fileformat=VCFv4.2
##contig=<ID=MN908947,length=29903>
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample
MN908947 210 1 G T . PASS primer_calls_ignored=0/0;total_primer_bases=0/0;unfiltered_depth=34;total=33/1;amplicon_overlap=1;amplicon_totals=33/1;amplicon_names=SARSCoV_1200_1 GT 1/1
MN908947 28247 28 AGATTTC A . low_frs primer_calls_ignored=0/0;total_primer_bases=0/0;unfiltered_depth=633;total=601/32;amplicon_overlap=1;amplicon_totals=601/32;amplicon_names=SARSCoV_1200_28 GT 1/1

Things that are specific to the sample under analysis , and not the variant, need to be in the final column, so i think that first line needs to become

MN908947 210 1 G T . PASS GT:PRIMER_CALLS_IGNORED:TOTAL_PRIMER_BASES:UNFILTERED_DEPTH:UNFILTERED_DEPTH_BY_ALLELE:AMPLICON_OVERLAP:AMPLICON_TOTALS:AMPLICON_NAMES 1/1:0/0:0/0:33/1:1:33/1:SARSCoV_1200_1

(the genotype has to be the first thing in that last column, then i've left your other stuff unchanged except they need to be upper case)

So i think the changes are

• add definitions of PRIMER_CALLS_IGNORED etc in the header, and move them all to colon-separated things in the final column. oh and i renamed totals as UNFILTERED_DEPTH_BY_ALLELE, so it's a bit clearer.

• ideally add depth on the alleles we have in the 4th and 5th columns. Let's say the ref allele is A, and the alt is C, it would be good to have the good coverage on those two alleles, like "1,20", where 1 is ref and 20 is alt. Note i really mean ref here, not consensus.