weird characters in GATK vcf tables
I have created a vcf table using GATK using haplotypeCaller, genomicsDBimpirt and genotypesVCF.
the output I get is very different from the vcf4.2 format.
0/1:8,3:11:36:36,0,233 from vcftools
0|1:2,4:6:72:0|1:4938136_T_C:162,0,72:4938136 #from GATK ^_____________^ ^_____^ 0|1:2,4:6:72:0:162,0,72 #how it should look like...
This format stuck the downstream pipeline I am used to work with.
Any idea what is it mean / how to get rid of it?
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