vcf-consensus with more than one alternative alleles

Question

[iraun]

Hi all,
If I have a vcf file, and some variants have more than one alternative alleles, like:

#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT
Chr_3.1    124358    .    G    GCCCC,GCC    32.2    .    INDEL;IS=2,0.200000;DP=10;VDB=6.695005e-02;AF1=1;AC1=2;DP4=0,0,1,2;MQ=60;FQ=-40.5    GT:PL:DP:GQ    1/1:104,39,33,69,0,66:3:10

How can I know which one is adding vcf-consensus to the new reference?

Thanks in advance.

Answer 1

[Pierre Lindenbaum]

it uses the first ALT: http://sourceforge.net/p/vcftools/code/HEAD/tree/trunk/perl/vcf-consensus

$alt = ($idx=index($$vline[4],','))==-1 ? $$vline[4] : substr($$vline[4],0,$idx);

[iraun]

Hi Pierre! Thanks! Do you know if it adds the first one because the vcf file always put in the first position the "best" alt or... "by chance"?

[Pierre Lindenbaum]

the spec doesn't say anything about the order: http://samtools.github.io/hts-specs/VCFv4.2.pdf

[iraun]

Ok...so...I don't understand why vcf-consensus chooses the first alt to insert into de reference... I mean, maybe the second one is the "most representative" allele... but..thanks for the links and useful information!