domains / families / science / pileup-generation

pileup-generation

separate

Generate pileup data for variant calling using samtools mpileup and pysam. Use when preparing data for variant calling, analyzing per-position read data, or calculating allele frequencies.

When to use

• preparing data for variant calling
• analyzing per-position read data
• calculating allele frequencies
• counting alleles at a position
• coverage analysis
• SNP/indel detection

When not to use

• Germline WGS / WES production
• Somatic SNV/indel
• Long-read small variants
• Long-read SV
• Ultra-low-frequency (ctDNA / MRD)

Skill page

Source