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Question: Dataset format conversion from fastq to bam and vcf
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gravatar for gvacinova
14 months ago by
gvacinova • 0
gvacinova • 0 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 • 1.5k views
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modified 14 months ago by Jennifer Hillman Jackson ♦ 25k • written 14 months ago by gvacinova • 0
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gravatar for Jennifer Hillman Jackson
14 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 14 months ago by Jennifer Hillman Jackson ♦ 25k
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