weird characters in GATK vcf tables

0

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.

for example:

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?

thanks!


genomics


bioinformatics

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