Question: Set minimum variant frequency while calling variants with samtools
0
gravatar for kspata
4 months ago by
kspata50
Chicago
kspata50 wrote:

Hi All,

Currently I am using following command to call variants using samtools/bcftools.

samtools mpileup -d 1000000 -L 1000000 -uf ref.fasta sample.sorted.bam | bcftools view -vcg  - > sample.SAMtools.vcf

What I want is to report the variants present at and above 1% variant frequency in the vcf file. I looked into both mpileup, bcftools view, and bcftools call manual but could not find any parameter to set variant frequency.

This option is available in freebayes (-F 0.01) and VarScan (--min-var-freq 0.01).

How can I set these parameters for samtools and know what default parameters are used?

Thanks!!

ADD COMMENTlink modified 4 months ago by Istvan Albert ♦♦ 80k • written 4 months ago by kspata50
0
gravatar for Istvan Albert
4 months ago by
Istvan Albert ♦♦ 80k
University Park, USA
Istvan Albert ♦♦ 80k wrote:

You can filter your VCF file as it is being produced with bcf filter

ADD COMMENTlink modified 4 months ago • written 4 months ago by Istvan Albert ♦♦ 80k

Hi Istvan,

I tried the following command but it does not seem to work.

 samtools mpileup -d 1000000 -L 1000000 -uf ref.fasta Sample.sorted.bam | bcftools view -vcg -i 'MAF[*] >= 0.5'  - > Sample.SAMtools_VF50.vcf

This should give me the variants present at > 50 % frequency but all variants are reported even those which are less than 50%.

Can you please give me an example of the bcf filter command which you mentioned?

ADD REPLYlink written 4 months ago by kspata50
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1083 users visited in the last hour