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Question: VCF output from Mpileup tool
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gravatar for felipe_o_torquato
2.4 years ago by
felipe_o_torquato • 10
felipe_o_torquato • 10 wrote:

Hi everyboy,

I am trying to call SNP using the SAM Tools → mpileup in Galaxy.

Since the input in mpileupI is BAM format, I converted FASTQ file to BAM format using NGS: Mapping → Map with BWA.

Thereafter, I used this BAM file in mpileupI creating a compressed BCF file, which was converted to VCF using SAM Tools → bcftools call. However, when I immport the VCF to IGV it says that variants were not found.

I would like to know whats is going on since I would to see variants.

thanks in advance!
pileup igv galaxy mpileup vcf • 1.6k views
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modified 2.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.4 years ago by felipe_o_torquato • 10
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gravatar for felipe_o_torquato
2.4 years ago by
felipe_o_torquato • 10
felipe_o_torquato • 10 wrote:

Hello Jennifer,

we solved the problem. Many thanks!
ADD COMMENT • link written 2.4 years ago by felipe_o_torquato • 10
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gravatar for Jennifer Hillman Jackson
2.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Mpileup has an option to output VCF directly. On the tool form, see Choose the output format and select VCF.

For why the existing problem is occurring, this is difficult to know given this information. I always start by making certain that the exact same reference genome is used for the analysis and in external tools (like IGV). Worth a check, here is how: https://wiki.galaxyproject.org/Support#Reference_genomes

Please give these a try and let us know if you need more help! Cheers, Jen, Galaxy team
ADD COMMENT • link written 2.4 years ago by Jennifer Hillman Jackson ♦ 25k
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