Question: Dataset format conversion from fastq to bam and vcf
gravatar for gvacinova
14 months ago by
gvacinova0 wrote:


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 • 1.5k views
ADD COMMENTlink modified 14 months ago by Jennifer Hillman Jackson25k • written 14 months ago by gvacinova0
gravatar for Jennifer Hillman Jackson
14 months ago by
United States
Jennifer Hillman Jackson25k wrote:


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):

For future reference, Support FAQs can be reviewed here:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 14 months ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 180 users visited in the last hour