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vcf-consensus with more than one alternative alleles

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.

vcf-consensus vcf
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updated by Biostar Biostar • written by iraun iraun

1 answer

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);
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updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

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"?

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written by iraun 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!

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written by iraun iraun

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