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Question: BCFtools output tabular
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gravatar for fagrimal
4.1 years ago by
fagrimal • 0
fagrimal • 0 wrote:

Hi,

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 • 1.3k views
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modified 4.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.1 years ago by fagrimal • 0
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gravatar for Jennifer Hillman Jackson
4.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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 COMMENT • link written 4.1 years ago by Jennifer Hillman Jackson ♦ 25k
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