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FastaAlternateReferenceMaker chooses always first ALT nucleotide

edert8edert8 Member
edited September 2015 in Ask the GATK team

Hi,
I am using FastaAlternateReferenceMaker from GenomeAnalysisTK-3.4-46

my vcf-file looks like this:

#header...
##source=SelectVariants
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  sample11
scaffold-50 1055905 .   G   C,T,A   14632.70    PASS    AC=0,0,2;AF=0.00,0.00,1.00;AN=2;BaseQRankSum=-1.612;ClippingRankSum=-0.732;DP=56;FS=0.660;InbreedingCoeff=1.0000;MQ=60.00;MQ0=0;MQRankSum=-0.369;QD=30.79;ReadPosRankSum=0.672;SOR=0.742    GT:AD:DP:GQ:PL  3/3:0,0,0,56:56:99:2635,2647,2745,2635,2647,2635,178,184,178,0

this is how I start the program:

java -jar GenomeAnalysisTK.jar \
-T FastaAlternateReferenceMaker \
-R C17_ref.fna \
-o test.fasta \
-L scaffold-50:1055905-1055905 \
-V results/tmp/J65_clean.vcf

and the resulting fasta file will always have a C instead of an A which would be correct here (if i use A,T,C in the ALT column I will get an A). so it looks like the first ALT nucleotide is taken and it totally ignores the 3/3 in the last column (if I change it to 1/1 or 0/0 nothing changes)

What am I doing wrong?

Thanks

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