Question: Dataset format conversion from fastq to bam and vcf
0
gravatar for gvacinova
12 weeks ago by
gvacinova0
gvacinova0 wrote:

Hello,

I am a begginer in the galaxy and I want to ask you how can I convert fastq files to bam and vcf files.

Thank you very much,

Gabriela Vacínová

fastq convert vcf dataset bam • 118 views
ADD COMMENTlink modified 12 weeks ago by Jennifer Hillman Jackson23k • written 12 weeks ago by gvacinova0
0
gravatar for Jennifer Hillman Jackson
12 weeks ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

For fastq to bam, please see the tool NGS: Picard > FastqToSam convert Fastq data into unaligned BAM

For fastq to vcf (or bam to vcf), this is possible after the fastq sequences are aligned (mapped, producing a BAM/SAM dataset) and a tool that outputs a VCF dataset is run. Please see the Learn Galaxy tutorials for example workflows (example: Variant Analysis): https://galaxyproject.org/learn/

For future reference, Support FAQs can be reviewed here: https://galaxyproject.org/support/

Thanks! Jen, Galaxy team

ADD COMMENTlink written 12 weeks ago by Jennifer Hillman Jackson23k
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