Entering edit mode
2.6 years ago
rheab1230
▴
140
Hello everyone, I have 22 vcf file for each chr. They were in genome build hg19 so I did a liftover and convert them to hg38 genome build. Now I need just chrom and position values from these vcf files and merge them together into a separate coloumn to form chrom_pos. But in my case I am getting some added values. So i use linux awk command to extract chr and pos values. But when I see the output its coming very weird like it has some values corresponding to chr2 also. Like this:
chr2_KI270773v1_alt
chr2_KI270894v1_alt
Did you try googling to find out what these contigs are?
Yes, I did. They are related to hg38
"related to" is not a thing. Once you can be more specific about them, you'll understand what they are and why you're seeing these entries.