Hi Galaxy community,
I have a question regarding the tool ‘‘VCFtoTab-delimited.’’
The output tabular file somehow has double numbers of lines, compared to the input vcf file.
As I further look into the data, each line of the vcf file becomes two lines in the tabular.
That is to say, each ‘‘position’’ has two lines of information, named ‘‘Sample1’’ and ‘‘1.vcf.sorted_Sample1’’ in the SAMPLE COLUMN.The information of the variants calling data, such as ABQ, AD, FREQ, are also different.
Can anyone explain this to me? How this can happen and which line I should take as the ‘‘correct information’’, since I am looking for variants on specific genes as well as their VAF.
Thanks for your support.