pysam · GPTomics/bioSkills

Soft- or hard-clips PCR primer footprints from aligned amplicon BAMs so primer bases stop masquerading as confirmed reference sequence.

GPTomics/bioSkills

Filters BAM alignments by FLAG bits, mapping quality and regions with samtools view or pysam, with recipes for common keep and drop cases.

GPTomics/bioSkills

Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam.

GPTomics/bioSkills

Sort alignment files by coordinate or read name using samtools and pysam.

GPTomics/bioSkills

Generate alignment statistics using samtools flagstat, stats, depth, coverage, and mosdepth.

GPTomics/bioSkills

Annotate copy number variant segments with overlapping genes, dosage-sensitivity scores, cancer driver databases, population frequencies, and clinical-variant content.

GPTomics/bioSkills

Mark and remove PCR/optical duplicates using samtools fixmate and markdup.

GPTomics/bioSkills

Generate consensus sequences and manage reference files using samtools.

GPTomics/bioSkills

View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam.

GPTomics/bioSkills

Generate pileup data for variant calling using samtools mpileup and pysam.

GPTomics/bioSkills

Process many sequence files in batch (count, merge, split, convert, summarize) with memory-safe streaming and on-disk indexing using Biopython, pysam, or pyfastx.

GPTomics/bioSkills

Detects somatic mutations in circulating tumor DNA, treating low-VAF detection as a signal-versus-noise problem set by error suppression and molecules sampled, not by the choice of caller.

GPTomics/bioSkills