Question: VCF output from Mpileup tool
0
gravatar for felipe_o_torquato
24 months ago by
felipe_o_torquato10 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 • 1.2k views
ADD COMMENTlink modified 24 months ago by Jennifer Hillman Jackson25k • written 24 months ago by felipe_o_torquato10
1
gravatar for felipe_o_torquato
24 months ago by
felipe_o_torquato10 wrote:

Hello Jennifer,

we solved the problem. Many thanks!

ADD COMMENTlink written 24 months ago by felipe_o_torquato10
0
gravatar for Jennifer Hillman Jackson
24 months ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 24 months ago by Jennifer Hillman Jackson25k
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