Question: extracting one snp position from a vcd file
0
gravatar for evelyn
4 weeks ago by
evelyn90
evelyn90 wrote:

Hello,

Is there a way to extract one SNP by POS from a large vcf file.

Thank you!

snp • 37 views
ADD COMMENTlink modified 4 weeks ago by ATpoint31k • written 4 weeks ago by evelyn90

you asked many questions on this site. it would be nice if you could validate the correct answers (green ticks on the left).

ADD REPLYlink written 4 weeks ago by Pierre Lindenbaum127k
0
gravatar for ATpoint
4 weeks ago by
ATpoint31k
Germany
ATpoint31k wrote:

tabix, see the example in the manual: http://www.htslib.org/doc/tabix.html

Essentially you compress the file with bgzip, then index with tabix and then use tabix your.vcf.gz chr:start-end for retrieval.

ADD COMMENTlink written 4 weeks ago by ATpoint31k
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