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Find Rs# From Vcf

Hi all, I have a set of rs#, about 1500 or so and what i want to do is query my annotated VCF files which already has the dbSNP ids and create another VCF file with only those variants if they are found to be there.

i tried to use grep but i think it can only do one search term at a time, so how would i find all my rs#, I could put all the rs# in a single text file.

any ideas?

vcf
• 6,963 views • link
updated by pd3 pd3 • written by win win

Try grep -f file_with_set_of_rs# big_vcf_file > new_vcf.txt

Header will have to be added separately.

• 282 views • link
written by Ashutosh Pandey Ashutosh Pandey

and try: grep -wFf

• 228 views • link
written by brentp brentp

Cool. -F can be used to make it faster as no regex is involved.

• 0 views • link
written by Ashutosh Pandey Ashutosh Pandey

2 answers

duplicate of

Query a dbSNP VCF File

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Try `bcftools view -i'%ID=@path/to/ids.txt' file.vcf`

http://samtools.github.io/bcftools/bcftools.html

• 1 views • link
written by pd3 pd3

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