Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Call SNP crayfish Bioinformatics 2 10-29-2013 12:43 PM
How to call SNP using known SNP information nkwuji Bioinformatics 1 07-23-2013 10:16 PM
Sequence transposon flanking region Akira Sample Prep / Library Generation 8 03-18-2012 07:53 AM
1000 genome SNP call zhanglu295 Bioinformatics 5 03-30-2011 10:57 AM
SOLiD SNP CALL Problem pr0t3us Bioinformatics 2 03-17-2011 08:56 AM

Thread Tools
Old 07-24-2014, 06:49 AM   #1
Location: South Africa

Join Date: Jun 2013
Posts: 25
Default Extract flanking sequence of SNP call

Hi all.

I have mapped sequencing data to a reference using BWA and called SNP using samtools mpileup and generated a vcf using bcftools. What I would like to achieve is to extract the SNP along with a 35base flanking sequences. I would appreciate any help with this.

JdeBruin is offline   Reply With Quote
Old 07-24-2014, 07:03 AM   #2
Rick Westerman
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104

bedtools always comes to mind when asking questions like "how to extract sequence". It should be easy to convert the VCF single coordinate into the start & end coordinates for a BED file (Excel or other spreadsheet program or a simple Perl/Python script). Then use fastaFromBed.
westerman is offline   Reply With Quote
Old 07-24-2014, 05:06 PM   #3
Senior Member
Location: San Diego

Join Date: May 2008
Posts: 912

samtools faidx, when given genomic coordinates, will make a fasta of the desired region. That another way, using software you've already got.
swbarnes2 is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 04:32 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO