domains / families / science / bio-workflows-fastq-to-variants

bio-workflows-fastq-to-variants

separate

End-to-end DNA sequencing workflow from FASTQ files to variant calls. Covers QC, alignment with BWA, BAM processing, and variant calling with bcftools or GATK HaplotypeCaller.

When to use

• calling variants from raw sequencing reads
• QC and trimming with fastp
• alignment with BWA
• BAM processing including sorting and duplicate marking
• variant calling with bcftools
• variant calling with GATK HaplotypeCaller
• variant filtering

Skill page

Source