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FastaAlternateReferenceMaker chooses always first ALT nucleotide
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 \
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?