Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
snp calling with samtools maize Bioinformatics 2 03-26-2013 05:51 PM
problem with samtools and SNP calling lpn Bioinformatics 21 11-05-2012 12:08 PM
snp calling with bwa-samtools heiya Bioinformatics 3 08-21-2012 09:51 PM
Samtools SNP calling vidhya Bioinformatics 3 04-07-2011 06:17 AM
SAMtools and SNP calling Jan Bioinformatics 2 09-16-2010 01:01 PM

Thread Tools
Old 01-09-2019, 09:55 PM   #1
Junior Member
Location: India

Join Date: Mar 2017
Posts: 3
Default SNP calling using samtools

Hi all,

I have RNA-seq paired-end data from Illumina and I am using BWA-mem for mapping and samtools for SNP calling. I wanted to understand and get your opinion regarding following.

1. What is the criteria for calling the variant? Specifically, at a particular position, how many reads should contain variation for it to be called as a variant.
I want to call variant at a position if it supported by more than 20% of reads at that position.

What parameter can I use to achieve this.

Any help is appreciated!!
ankit4035 is offline   Reply With Quote
Old 01-10-2019, 06:32 AM   #2
Registered Vendor
Location: Eugene, OR

Join Date: May 2013
Posts: 523

You can filter your vcf for variants that fit your minor allele threshold with vcftools

From the docs:
--non-ref-af <float>
--max-non-ref-af <float>
--non-ref-ac <integer>
--max-non-ref-ac <integer>

--non-ref-af-any <float>
--max-non-ref-af-any <float>
--non-ref-ac-any <integer>
--max-non-ref-ac-any <integer>

Include only sites with all Non-Reference (ALT) Allele Frequencies (af) or Counts (ac) within the range specified, and including the specified value. The default options require all alleles to meet the specified criteria, whereas the options appended with "any" require only one allele to meet the criteria. The Allele frequency is defined as the number of times an allele appears over all individuals at that site, divided by the total number of non-missing alleles at that site.
Providing nextRAD genotyping and PacBio sequencing services.
SNPsaurus is offline   Reply With Quote
Old 01-10-2019, 07:07 PM   #3
Junior Member
Location: India

Join Date: Mar 2017
Posts: 3

Thanks, for the help.

I was thinking that I could restrict this during SNP calling and not after vcf file was generated. How dumb of me..
ankit4035 is offline   Reply With Quote

bcftools, mpileup, rnaseq, samtools, snp

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 02:41 AM.

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