Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
REF ALT conversion - multiple sample vcf > single sample vcf + trimAlternates
Dear GATK Team,
I have extracted the first sample of the following multiple sample vcf example:
chr1 3007281 . CCTT CT,C 3654.92 . AC=21,2;AF=0.157,0.015;AN=134;BaseQRankSum=1.47;ClippingRankSum=0.668;DP=10953;FS=7.789;GQ_MEAN=29.39;GQ_STDDEV=27.74;InbreedingCoeff=0.7055;MLEAC=22,2;MLEAF=0.164,0.015;MQ=60.93;MQ0=0;MQRankSum=-3.800e-01;NCC=0;QD=16.03;ReadPosRankSum=0.760;SOR=0.522;set=Intersection GT:AD:DP:GQ:PL 0/1:10,4,0:14:38:38,0,312,68,324,392 0/0:21,0,0:21:9:0,9,135,9,135,135
GenomeAnalysisTK.jar -nt 2 -T SelectVariants -trimAlternates -V $INPUT -R $R -o $OUTPUT -sn 1
and I get this:
chr1 3007281 . CCT C 3654.92 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.47;ClippingRankSum=0.668;DP=14;FS=7.789;GQ_MEAN=29.39;GQ_STDDEV=27.74;InbreedingCoeff=0.7055;MQ=60.93;MQ0=0;MQRankSum=-3.8
00e-01;NCC=0;QD=16.03;ReadPosRankSum=0.760;SOR=0.522;set=Intersection GT:AD:DP:GQ:PL 0/1:10,4:14:38:38,0,312
The question is why I get C as the ALT allele by using trimAlternates?
Thank you in anticipation