Question: vcf-consensus with more than one alternative alleles
0
gravatar for iraun
5.5 years ago by
iraun3.6k
Norway
iraun3.6k wrote:

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 • 1.8k views
ADD COMMENTlink modified 4.6 years ago by Biostar ♦♦ 20 • written 5.5 years ago by iraun3.6k
2
gravatar for Pierre Lindenbaum
5.5 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum124k wrote:

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);
ADD COMMENTlink modified 8 weeks ago by RamRS25k • written 5.5 years ago by Pierre Lindenbaum124k

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"?

ADD REPLYlink written 5.5 years ago by iraun3.6k

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

ADD REPLYlink written 5.5 years ago by Pierre Lindenbaum124k

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!

ADD REPLYlink written 5.5 years ago by iraun3.6k
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