Stars in GT, incompatible with SnpSift
I have questions about the combination genotypeGVCFs/SelectVariants.
I have some loci with the genotype 0/2 for some samples, 0/1 for other.. There is thus two different alleles , but the corresponding ALT is for example « G,*_». If the nucleotide G corresponds to 0/1, to what corresponds exactly the 0/2 ? Said otherly, what does this star mean ?
How to correctly extract the variants for each sample from the combined vcf ? For a given sample, my command line is :
java -jar GenomeAnalysisTK.jar -T SelectVariants -R hg19_min_oldM.fa -V Combined.vcf -o Sample.vcf --excludeNonVariants -sn Sample
Nevertheless, it gives a vcf which is not exploitable by SnpSift extractFields because of theses stars.
- last question : I read that a downsampling is effectuated by SelectVariants, but I do not understand what it means. As you guess, I really want to conserve all the variants that have been called by HaplotypeCaller, so I don't want SelectVariants to perform an other thing that extracting all the variants from each sample....
Sorry for all these questions... but thanks by advance to who will help me !