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I have a zipped vcf file of dbSNP hg38 version

No space left on my device to unzip that

I want to extract a column from that

I have tried this

cut -f 3 00-All.vcf.gz | sed 's/[\t]/,/g' > cols.csv

But that needs my vcf to be unzipped

Do you know any solution please?

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1 Answer 1

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Either the zcat command or gunzip -c will decompress the file in a streaming fashion to the standard output without writing the decompressed data to disk. Pipe the output to cut, sed, etc.

Try

zcat 00-All.vcf.gz | cut -f 3 | sed 's/[\t]/,/g' > cols.csv

or

gunzip -c 00-All.vcf.gz | cut -f 3 | sed 's/[\t]/,/g' > cols.csv

But if you just want a single 'column' (I presume you mean field), then you are better off just doing bcftools query.

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    $\begingroup$ On some systems I have issues with zcat but gunzip -c will also accomplish the same result. $\endgroup$
    – Daniel Standage
    Jan 26, 2022 at 15:38
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    $\begingroup$ @Exhausted Don't use unix utilities for this - it needs a level of expertise that your post history suggests you do not have. Use bcftools instead, that will address a lot of edge cases that you can't foresee. $\endgroup$
    – Ram RS
    Jan 26, 2022 at 19:44
  • $\begingroup$ tar can do select zip file search and extraction, but you're also data munging. $\endgroup$
    – M__ ♦
    Jan 26, 2022 at 20:47
  • $\begingroup$ Thank you all, but why you down voting me? $\endgroup$
    – Exhausted
    Jan 27, 2022 at 11:10
  • $\begingroup$ I have No idea, I didn’t downvote. $\endgroup$
    – user438383
    Jan 27, 2022 at 11:29

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