If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!
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.
I am trying to select heterozygotes from the VCF file. I use this command many times and it works all the time. But something error pops up this time, do not know what is the problem. I check the documentary and seems like syntax is right because I use it all the time
1) partial data line information is like this
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 4751_42R
chr10 3101362 rs33880920 G C 189.60 . ABHom=1.00;AC=0;
;MQ=57.19;MQ0=0;MQRankSum=-0.742;QD=31.60;ReadPosRankSum=0.742 GT ./.
chr10 3101529 rs29314734 C T 116.56 . ABHet=0.500;ABHo
=-0.271 GT ./.
2) when I run
$ java -Xmx20g -jar /hpf/tools/centos6/gatk/3.6.0/GenomeAnalysisTK.jar -T SelectVariants -R genome.fa --variant 4751_42map.vcf -select 'vc.getGenotype("4751_42R”).isHet()' -o 4751_42maph.vcf
3) Error is