Question: BCFtools output tabular
gravatar for fagrimal
3.7 years ago by
fagrimal0 wrote:


I'm sorry for my naive question (but this is my first analysis)...

Analysis: 19 PCR targetting exons (1 protein)

Fastq aligned by BWA (with genome reference hg19) (output SAM) > SAMtools (SAM-to-BAM) (output BAM) > Mpileup SNP and indel caller (output bcf) then

BCFtools, want to convert BCF format to VCF but output is tabular. Why?

I want visualization and exploring using IGV. How?

Thank you for your help


tool usage vcf mpileup samtools • 1.2k views
ADD COMMENTlink modified 3.7 years ago by Jennifer Hillman Jackson25k • written 3.7 years ago by fagrimal0
gravatar for Jennifer Hillman Jackson
3.7 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The Mpileup tool creates two types of output.

The first is from "Basic" usage and is tabular that can be reassigned to "mpileup" datatype for downstream analysis. I suspect this is what you created. 

The second is from "Set advanced options: Advanced" where the option "Genotype Likelihood Computation:" is set to perform the calculation this way. This creates "bcf" output.

Please give this a try and see if it resolves the issue. Best, Jen, Galaxy team

ADD COMMENTlink written 3.7 years ago by Jennifer Hillman Jackson25k
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