vcf file analysis
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8 weeks ago
rheab1230 ▴ 30

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
columns rsid vcf position • 263 views
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Did you try googling to find out what these contigs are?

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Yes, I did. They are related to hg38

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"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.

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